PBMC: Sampling Time-Dependent Single-Cell Transcriptional Signature
10/21/2019
1 Introduction
The objective of this notebook is to characterize the transcriptional signature associated with time at room temperature (RT) until cryopreservation in Peripheral Blood Mononuclear Cells (PBMC). We hypothesize that, as we are extracting blood cells from its physiological niche (~37ºC) and placing them at RT (~21ºC), they will express a transcriptional signature that allows them to cope with the change in temperature.
2 Pre-processing
2.1 Package loading
library(scater)
library(scran)
library(Seurat)
library(ggpubr)
library(biomaRt)
library(org.Hs.eg.db)
library(AnnotationDbi)
library(GOplot)
library(GOstats)
library(topGO)
library(ggrepel)
library(ggridges)
library(viridis)
library(pheatmap)
library(readxl)
library(tidyverse)2.2 Source script with functions
source("bin/utils.R")2.3 Load data
We dispose of a demultiplexed, filtered, normalized and annotated Seurat object that contains the transcriptome and metadata of >10,000 PBMC from two donors (male/female) that were kept at varying times at RT (0h, 2h, 8h, 24h, 48h).
pbmc <- readRDS("results/R_objects/10X_pbmc_Seurat_clustered.RDS")
pbmc <- subset(pbmc, subset = condition %in% c("0h", "2h", "8h", "24h_RT", "48h_RT"))
pbmc$time <- factor(pbmc$condition, levels = c("0h", "2h", "8h", "24h_RT", "48h_RT"))
levels(pbmc$time) <- c("0h", "2h", "8h", "24h", "48h")
Idents(pbmc) <- "cell_type"
DimPlot(pbmc)
3 Transcriptional signature
To find the transcriptional signature associated with time, we will conduct a differential expression analysis between time-biased and time-unbiased cells. Such distinction is based on our previous results, which show that cells that are kept >2h at RT prior to cryopreservation possess altered transcriptional landscapes in comparison to those left for <=2h.
We will opt to use a wilcoxon test. Despite the fact that there are recent methods that are tailored to scRNA-seq DE, recent benchmarking suggest that (1) wilcoxon test is still among the best-performing tools and (2) with scran normalization there is no need for tailored methods.
First, let us assess the differential expression analysis for all cell types together:
pbmc$is_biased <- ifelse(pbmc$time %in% c("0h", "2h"), "unbiased", "biased")
Idents(pbmc) <- "is_biased"
dea_general <- FindMarkers(pbmc, ident.1 = "biased", test.use = "wilcox")
dea_general <- dea_general %>%
rownames_to_column(var = "gene") %>%
dplyr::mutate(is_significant = ifelse(p_val_adj < 0.001, TRUE, FALSE))
genes <- rownames(pbmc[["RNA"]]@data)
avg_expr <- rowMeans(as.matrix(pbmc[["RNA"]]@data))
log2_fc <- apply(as.matrix(pbmc[["RNA"]]@data), 1, function(x) {
mean_unbiased <- mean(x[pbmc$is_biased == "unbiased"]) + 1
mean_biased <- mean(x[pbmc$is_biased == "biased"]) + 1
log2(mean_biased / mean_unbiased)
})
is_significant <- ifelse(genes %in% dea_general$gene[dea_general$is_significant], TRUE, FALSE)
dea_all <- data.frame(
gene = genes,
average_expression = avg_expr,
log2_fc = log2_fc,
is_significant = is_significant
)
subset_sig <- dplyr::filter(dea_all, is_significant & log(average_expression + 1) > 0.5 & abs(log2_fc) > 0.2)
top_up <- as.character(subset_sig$gene[subset_sig$log2_fc > 0])
top_down <- subset_sig %>%
dplyr::arrange(log2_fc)
top_down <- as.character(top_down$gene[1:10])
subset_sig <- dplyr::filter(subset_sig, gene %in% c(top_up, top_down))
ma_plot_all <- dea_all %>%
ggplot(aes(log(average_expression + 1), log2_fc, color = is_significant)) +
geom_point(size = 0.85, alpha = 0.6) +
geom_smooth(method = "loess", color = "darkblue") +
geom_hline(yintercept = 0, color = "black", linetype = "dashed") +
scale_color_manual(values = c("gray78", "green4"), labels = c("sig", "no sig")) +
labs(x = "log (Average Expression)", y = "log (biased / unbiased)", color = "") +
theme_classic2() +
theme(axis.title = element_text(size = 11),
legend.text = element_text(size = 11),
plot.title = element_text(hjust = 0.5, face = "bold"))
ma_plot_all +
geom_text_repel(data = subset_sig, aes(label = gene), color = "black") 
# saveRDS(ma_plot_all, "results/R_objects/ggplots/ma_plot_all_types_pbmc.rds")
dea_all <- arrange(dea_all, desc(abs(log2_fc)))
DT::datatable(dea_all)# saveRDS(dea_general$gene, "results/R_objects/cold_shock_signature.rds")
# saveRDS(dea_general$gene[dea_general$avg_logFC > 0], "results/R_objects/cold_shock_signature_up.rds")
# saveRDS(dea_all, "results/R_objects/dea_results_pbmc.rds")Overall, we detected a total of 236 differential expressed genes (DEG), 61 of which were upregulated and 175 were downregulated.
Important: note that some analysis were recomputed in the directory “4-REVISION” to answer concerns raised by reviewer 2.
Let’s visualize the same information with a dot plot:
expr_matr <- scale(as.matrix(pbmc[["RNA"]]@data), TRUE, TRUE)
meta_df <- data.frame(
time = c(),
gene = c(),
expression = c(),
fraction_expr = c()
)
times <- c("0h", "2h", "8h", "24h", "48h")
genes <- c(top_down, top_up)
for (t in times) {
for (g in genes) {
cells <- colnames(pbmc)[pbmc$time == t]
expr <- mean(expr_matr[g, cells])
frc_expr <- mean(as.numeric(pbmc[["RNA"]]@counts[g, cells]) != 0)
current_df <- data.frame(
gene = g,
time = t,
expression = expr,
fraction_expr = frc_expr
)
meta_df <- rbind(meta_df, current_df)
}
}
dotplot <- meta_df %>%
group_by(gene) %>%
mutate(scaled_expression = (expression - mean(expression)) / sd(expression)) %>%
ungroup() %>%
mutate(gene = factor(gene, levels = genes)) %>%
ggplot(aes(x = time, y = gene, color = scaled_expression, size = fraction_expr)) +
geom_point() +
scale_colour_gradientn(colours = c("blue","white","red")) +
labs(x = "", y = "") +
theme_classic() +
theme(axis.text = element_text(size = 13),
legend.text = element_text(size = 13),
legend.title = element_text(size = 13),
legend.position = "bottom",
legend.box = "vertical")
dotplot
# saveRDS(dotplot, file = "results/R_objects/ggplots/dotplot_top_genes_signature.rds")Number of detected genes across time intervals:
pbmc$processing <- case_when(
pbmc$time %in% c("0h", "2h") ~ "fresh",
pbmc$time == "8h" ~ "local",
pbmc$time %in% c("24h", "48h") ~ "central"
)
df_supp_fig <- dplyr::select(pbmc@meta.data, "processing", "nFeature_RNA")
# saveRDS(df_supp_fig, "results/R_objects/ggplots/dataframe_ngenesVSprocessing_pbmc.rds")
palette <- c("#999999", "#92e8df", "#632c63", "#e4624e", "#c0e212")
n_detect_genes <- pbmc@meta.data %>%
mutate(is_biased = factor(is_biased, c("unbiased", "biased"))) %>%
ggplot(aes(is_biased, nFeature_RNA, fill = is_biased)) +
geom_boxplot() +
labs(x = "", y = "Number of Detected Genes") +
theme_classic() +
theme(legend.position = "none")
n_detect_genes
t <- t.test(
nFeature_RNA ~ is_biased,
data = pbmc@meta.data,
alternative = "two.sided"
)
t$p.value## [1] 3.909234e-159Then, we will perform the analysis for each cell type separately, as this will allow us to elucidate the specificity of the signature downstream:
pbmc_types <- SplitObject(pbmc, split.by = "cell_type")
pbmc_types <- purrr::map(pbmc_types, pre_process_seurat)
dea_list <- purrr::map(pbmc_types, function(seurat) {
seurat$is_biased <- ifelse(seurat$time %in% c("0h", "2h"), "unbiased", "biased")
Idents(seurat) <- "is_biased"
dea <- FindMarkers(seurat, ident.1 = "biased", test.use = "wilcox", logfc.threshold = 0, min.pct = 0)
dea <- dea %>%
rownames_to_column(var = "gene") %>%
mutate(is_significant = ifelse(p_val_adj < 0.001, TRUE, FALSE))
avg_expr <- rowMeans(as.matrix(seurat[["RNA"]]@data[dea$gene, ]))
dea$avg_expr <- avg_expr
dea
})
DT::datatable(dea_list$Monocyte)DT::datatable(dea_list$T)DT::datatable(dea_list$NK)DT::datatable(dea_list$B)# saveRDS(dea_list, "results/R_objects/dea_results_per_cell_type.rds")
# dea_list <- readRDS("results/R_objects/dea_results_per_cell_type.rds")Let us assess the overall distribution of the diferentially expressed genes (DEG) with an MA plot:
ma_plot_list <- purrr::map2(dea_list, names(dea_list), function(dea, donor) {
subset_sig <- filter(dea, is_significant & log(avg_expr + 1) > 0.4 & abs(avg_logFC) > 0.5)
dea %>%
ggplot(aes(log(avg_expr + 1), avg_logFC, color = is_significant)) +
geom_point() +
geom_smooth(method = "loess", color = "darkblue") +
geom_hline(yintercept = 0, color = "black", linetype = "dashed") +
geom_text_repel(data = subset_sig, aes(label = gene), color = "black") +
scale_color_manual(values = c("gray78", "green4"), labels = c("sig", "no sig")) +
labs(title = donor, x = "log (Average Expression)", y = "log (biased / unbiased)", color = "") +
theme_classic2() +
theme(axis.title = element_text(size = 11),
legend.text = element_text(size = 11),
plot.title = element_text(hjust = 0.5, face = "bold"))
})
ma_plot_list## $Monocyte
##
## $T
##
## $NK
##
## $B
Of note, we observe a very strong upregulation of FTH1 in all cell types. This gene encodes the heavy subunit of ferritin, whose function is to maintain intracellular iron balance. This function is particularly important in oxidative stress conditions (likely present in our study), as an excess of iron can increase the formation of reactive oxygen species (ROS). Thus, the time-dependent upregulation of FTH1 observed until 24h can serve as a protective mechanism against such stress. Moreover, in most cell types we also observe the upregulation of Cold Inducible RNA Binding Protein (CIRBP) which is the master regulator of the response to cold-shock:
Idents(pbmc) <- "time"
RidgePlot(pbmc, features = c("CIRBP"))
Thus, this is consistent with the fact that we are taking cells out of its physiological niche (~37ºC) and placing them at RT (~20ºC). Furthermore:
pbmc$is_biased <- ifelse(pbmc$time %in% c("0h", "2h"), "unbiased", "biased")
pbmc@meta.data %>%
mutate(is_biased = factor(is_biased, levels = c("unbiased", "biased"))) %>%
ggplot(aes(is_biased, nFeature_RNA, fill = is_biased)) +
geom_boxplot() +
labs(x = "", y = "# Detected Genes") +
theme_classic() +
theme(legend.position = "none")
In the biased samples there is an increased dropout rate and a decreased number of detected genes. This can be attributed to a lowered rate of transcription given the cold shock.
Finally, we also speculate that some genes increase their expression due to ex vivo incubation (and independently of the temperature). For instance, the up-regulation of CXCR4 suggests a lack of exposure of its ligand (CXCL12) in the lymph node microenvironment.
4 Cell type specificity
deg_100 <- purrr::map(dea_list, ~.x$gene[1:100])
deg_100 <- deg_100[levels(pbmc$cell_type)]
names(deg_100) <- c("T-cell", "NK", "Monocyte", "B-cell")
all_genes <- Reduce(union, deg_100)
cell_types <- names(deg_100)
matr_meta <- matrix(, nrow = length(all_genes), ncol = length(cell_types))
for (i in 1:length(all_genes)) {
new_row <- as.numeric(map_dbl(deg_100, ~ all_genes[i] %in% .))
matr_meta[i, ] <- new_row
}
rownames(matr_meta) <- all_genes
colnames(matr_meta) <- names(deg_100)
matr_meta <- matr_meta[order(rowSums(matr_meta), decreasing = TRUE), ]
cols <- colorRampPalette(c("gray99", "blue4"))(2)
heatmap_metasignatures <- pheatmap(
matr_meta,
color = cols,
cluster_rows = FALSE,
cluster_cols = FALSE,
fontsize = 5,
gaps_col = 1:4,
legend = FALSE,
show_rownames = FALSE,
show_colnames = TRUE,
fontsize_col = 12,
angle_col = 45
)
print(heatmap_metasignatures)
# saveRDS(object = heatmap_metasignatures, file = "results/R_objects/ggplots/heatmap_deg_pbmc.rds")
# saveRDS(object = deg_100, file = "results/R_objects/deg_100_pbmc.rds")Cell-type signatures:
# Score with cell type-specific markers
pbmc0 <- subset(pbmc, subset = time == "0h")
Idents(pbmc0) <- "cell_type"
markers <- FindAllMarkers(pbmc0, test.use = "wilcox")
markers$male[markers$male$cluster == "2", ]## NULLt_cell_mark <- c("CD3D", "IL7R", "LTB", "CD3E", "FCER1G", "TYROBP")
nk_mark <- c("GNLY", "NKG7", "GZMB", "FGFBP2", "CST7", "KLRF1", "GZMA", "CTSW", "CCL4", "SPON2", "PSMA1")
monocyte_mark <- c("S100A9", "LYZ", "S100A8", "CST3")
b_mark <- c("IGLL5", "CD79A", "MS4A1", "TCL1A", "CD79B", "HLA-DQA1", "LINC00926", "FCER2", "BANK1",
"VPREB3", "CD19", "BLK", "CD22", "IGJ", "TLR10", "BLNK")
markers_list <- list(t_cell = t_cell_mark, nk = nk_mark, monocyte = monocyte_mark, b = b_mark)
pbmc_types <- purrr::map(pbmc_types, function(seurat) {
seurat <- AddModuleScore(
seurat,
features = markers_list,
name = c("t_score", "nk_score", "monocyte_score", "b_score")
)
seurat
})
#
selected_scores <- c("t_score1", "nk_score2", "monocyte_score3", "b_score4")
pbmc_types <- pbmc_types[c("T", "NK", "Monocyte", "B")]
ridge_df <- purrr::map2(pbmc_types, selected_scores, function(seurat, score) {
df <- data.frame(
time = factor(seurat$time, levels = rev(levels(seurat$time))),
is_biased = factor(seurat$is_biased, levels = c("unbiased", "biased")),
cell_type_score = seurat@meta.data[, score]
)
df
})
new_names <- c("T-cell", "NK", "Monocyte", "B-cell")
names(ridge_df) <- new_names
ridge_gg_l <- purrr::map2(ridge_df, names(ridge_df), function(df, title) {
p <- ggplot(df, aes(cell_type_score, time, fill = is_biased)) +
geom_density_ridges() +
scale_fill_manual(values = c("azure3", "firebrick2")) +
labs(title = title, x = "Cell type score", y = "", fill = "") +
theme_classic() +
theme(plot.title = element_text(hjust = 0.5, size = 12))
p
})
ridge_gg_l$`T-cell` <- ridge_gg_l$`T-cell` +
scale_x_continuous(breaks = c(-1, 0, 1)) +
theme(axis.text.y = element_text(size = 11),
axis.title.x = element_blank(),
plot.margin = unit(c(0.3,0,0.25,0), units = "cm"))
ridge_gg_l$NK <- ridge_gg_l$NK +
theme(axis.line.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.title.x = element_blank(),
plot.margin = unit(c(0.3,0,0.25,0), units = "cm"))
ridge_gg_l$Monocyte <- ridge_gg_l$Monocyte +
theme(axis.line.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.title.x = element_blank(),
plot.margin = unit(c(0.3,0,0.25,0), units = "cm"))
ridge_gg_l$`B-cell` <- ridge_gg_l$`B-cell` +
theme(axis.line.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.title.x = element_blank(),
plot.margin = unit(c(0.3,0,0.25,0), units = "cm"))
leg <- as_ggplot(get_legend(ridge_gg_l$`B-cell` + theme(legend.position = "bottom")))
# ggsave(
# filename = "../doc/figures/legends/ridge_plot_legend.pdf",
# plot = leg,
# width = 9,
# height = 5,
# units = "cm"
# )
ridge_gg_arr <- ggarrange(
plotlist = ridge_gg_l,
nrow = 1, ncol = 4,
legend = "none",
widths = c(1,0.8,0.8,0.8,0.8)
)
ridge_gg_arr
# saveRDS(ridge_gg_arr, "results/R_objects/ggplots/ridge_plot_scores.rds")These results suggest that (1) the gene signatures are partially cell type-specific and (2) cells lose their identity in a time-dependent manner.
5 Gene Ontology Enrichment
All cell types:
top_list <- list(
down = dea_general$gene[dea_general$avg_logFC < 0],
up = dea_general$gene[dea_general$avg_logFC > 0],
universe = rownames(pbmc)
)
top_entrez <- purrr::map(top_list, function(x) {
entrez <- AnnotationDbi::select(
x = org.Hs.eg.db,
keys = x,
keytype = "SYMBOL",
columns = "ENTREZID"
)$ENTREZID
entrez <- entrez[!is.na(entrez)]
entrez
})
top_go <- purrr::map(
top_entrez[c("down", "up")],
get_GOenrichment,
universe = top_entrez$universe
)
top_go <- purrr::map(top_go, function(go) {
selection <- go$Size >= 3 & go$Size <= 600 & go$Count >= 5 & go$OddsRatio > 2 & go$Pvalue < 0.05
go <- go[selection, ]
go[order(go$OddsRatio, decreasing = TRUE), ]
})
top_go_rbind <- bind_rows(top_go, .id = "direction")
# WriteXLS::WriteXLS(top_go_rbind, "results/tables/go_pbmc_all.xlsx", SheetNames = "PBMC")
top_go <- top_go %>%
purrr::map(~ .x[1:2, ]) %>%
bind_rows(.id = "direction")
top_go_gg <- top_go %>%
mutate(direction = factor(direction, levels = c("up", "down")),
Term = factor(Term, levels = rev(top_go$Term))) %>%
ggplot(aes(Term, -1 * log10(Pvalue), color = direction)) +
geom_segment(aes(x = Term, xend = Term, y = 0, yend = -1 * log10(Pvalue))) +
geom_point() +
scale_color_manual("", values = c("firebrick3", "dodgerblue3")) +
labs(x = "", y = "-log10 (p-value)", color = "") +
theme_light() +
coord_flip()
top_go_gg
# saveRDS(object = top_go_gg, "results/R_objects/ggplots/lollipop_go_enrichment_pbmc.rds")Cell type-specific:
deg_cell_type <- purrr::map(dea_list, function(df) {
df_down <- df[df$avg_logFC < 0, ]
df_up <- df[df$avg_logFC > 0, ]
out_list <- list(down = df_down$gene[1:200], up = df_up$gene[1:200])
})
deg_cell_type_entrez <- purrr::map(deg_cell_type, function(l) {
entrez_l <- purrr::map(l, function(x) {
entrez <- AnnotationDbi::select(
x = org.Hs.eg.db,
keys = x,
keytype = "SYMBOL",
columns = "ENTREZID"
)$ENTREZID
entrez <- entrez[!is.na(entrez)]
entrez
})
entrez_l
})
universe_entrez <- AnnotationDbi::select(
x = org.Hs.eg.db,
keys = rownames(pbmc),
keytype = "SYMBOL",
columns = "ENTREZID"
)$ENTREZID
go_cell_type <- purrr::map(deg_cell_type_entrez, function(l) {
go <- purrr::map(l, function(deg_list) {
get_GOenrichment(target = deg_list, universe = universe_entrez)
})
})
go_cell_type_filt <- purrr::map(go_cell_type, function(l) {
go_filt <- purrr::map(l, function(go) {
selection <- go$Size >= 3 & go$Size <= 600 & go$Count >= 5 & go$OddsRatio > 2 & go$Pvalue < 0.05
go <- go[selection, ]
go[order(go$OddsRatio, decreasing = TRUE), ]
})
go_filt
})
go_cell_type_filt## $Monocyte
## $Monocyte$down
## GOBPID Pvalue OddsRatio ExpCount Count Size Term
## 291 GO:0007159 4.564589e-05 16.031056 0.4189803 5 20 leukocyte cell-cell adhesion
## 292 GO:0034314 4.827940e-05 15.828343 0.4238019 5 20 Arp2/3 complex-mediated actin nucleation
## 355 GO:0006120 2.117203e-07 12.850415 0.9109496 9 43 mitochondrial electron transport, NADH to ubiquinone
## 428 GO:0030838 1.893861e-07 10.775733 1.1715095 10 55 positive regulation of actin filament polymerization
## 429 GO:0032981 1.893861e-07 10.775733 1.1715095 10 55 mitochondrial respiratory chain complex I assembly
## 439 GO:0021762 3.245639e-04 9.827629 0.6177050 5 29 substantia nigra development
## 506 GO:0042773 5.653366e-08 9.182842 1.6188131 12 76 ATP synthesis coupled electron transport
## 507 GO:0008064 1.803405e-09 8.997255 2.0874169 15 98 regulation of actin polymerization or depolymerization
## 519 GO:0035722 1.801642e-04 8.363861 0.8520069 6 40 interleukin-12-mediated signaling pathway
## 520 GO:0038096 5.402030e-06 8.221785 1.3137859 9 62 Fc-gamma receptor signaling pathway involved in phagocytosis
## 521 GO:0098869 7.450219e-04 7.987879 0.7338431 5 35 cellular oxidant detoxification
## 571 GO:0046209 2.714268e-04 7.682797 0.9159074 6 43 nitric oxide metabolic process
## 572 GO:0070671 2.714268e-04 7.682797 0.9159074 6 43 response to interleukin-12
## 574 GO:0098754 3.165365e-05 7.508497 1.2567102 8 59 detoxification
## 575 GO:0043312 7.358333e-20 7.433697 7.9019584 42 373 neutrophil degranulation
## 576 GO:0002479 1.227153e-05 7.338776 1.4484117 9 68 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent
## 577 GO:0022900 7.437181e-09 7.330100 2.6625215 16 125 electron transport chain
## 580 GO:0042119 5.433856e-19 7.183026 7.9049556 41 375 neutrophil activation
## 584 GO:0042742 1.192117e-03 7.103934 0.8112927 5 39 defense response to bacterium
## 585 GO:0042136 3.955897e-04 7.103892 0.9798079 6 46 neurotransmitter biosynthetic process
## 587 GO:0032411 1.292017e-03 6.969884 0.8260066 5 39 positive regulation of transporter activity
## 588 GO:0002444 1.167789e-17 6.883636 7.7265519 39 369 myeloid leukocyte mediated immunity
## 589 GO:0002252 1.561691e-04 6.849728 1.1724418 7 71 immune effector process
## 593 GO:0002275 2.212016e-18 6.691929 8.6434290 42 408 myeloid cell activation involved in immune response
## 601 GO:0045333 2.603522e-05 6.602366 1.5860870 9 76 cellular respiration
## 642 GO:0045321 1.727748e-14 6.401825 6.8483419 33 346 leukocyte activation
## 644 GO:0048013 6.966268e-04 6.310579 1.0863088 6 51 ephrin receptor signaling pathway
## 647 GO:0006887 8.387089e-18 6.287744 9.4348968 43 449 exocytosis
## 650 GO:0009308 1.070452e-04 6.197482 1.4844039 8 70 amine metabolic process
## 657 GO:0046034 1.445854e-06 5.949516 2.5590943 13 121 ATP metabolic process
## 658 GO:0045454 9.477973e-04 5.913922 1.1502093 6 54 cell redox homeostasis
## 659 GO:0030595 2.491887e-03 5.911145 0.9545962 5 45 leukocyte chemotaxis
## 660 GO:0032760 2.495299e-03 5.908683 0.9548483 5 45 positive regulation of tumor necrosis factor production
## 708 GO:0019884 3.936281e-07 5.710078 3.0885250 15 145 antigen processing and presentation of exogenous antigen
## 709 GO:0048002 4.018884e-07 5.699665 3.0933728 15 146 antigen processing and presentation of peptide antigen
## 710 GO:0006521 3.007340e-03 5.635158 0.9956891 5 47 regulation of cellular amino acid metabolic process
## 711 GO:0051235 3.494218e-05 5.596951 2.0482707 10 98 maintenance of location
## 723 GO:0046903 1.272428e-14 5.366313 10.0586033 40 506 secretion
## 725 GO:0002576 1.608670e-03 5.283133 1.2710925 6 60 platelet degranulation
## 728 GO:0002263 2.665107e-15 5.231092 10.9963045 43 519 cell activation involved in immune response
## 733 GO:0032412 4.167429e-03 5.183794 1.0723562 5 51 regulation of ion transmembrane transporter activity
## 779 GO:0032956 3.342827e-06 5.062613 3.1926164 14 153 regulation of actin cytoskeleton organization
## 784 GO:1903555 2.097763e-04 4.902231 2.0661167 9 97 regulation of tumor necrosis factor superfamily cytokine production
## 785 GO:0007229 5.199431e-03 4.898934 1.1289091 5 53 integrin-mediated signaling pathway
## 795 GO:0006909 1.231139e-03 4.725485 1.6442092 7 81 phagocytosis
## 802 GO:0007005 1.630310e-05 4.661281 3.1821637 13 157 mitochondrion organization
## 810 GO:0010950 1.492565e-04 4.627773 2.4282197 10 114 positive regulation of endopeptidase activity
## 845 GO:0060337 7.482698e-03 4.455429 1.2297830 5 58 type I interferon signaling pathway
## 846 GO:0002504 3.541224e-03 4.451995 1.4829412 6 70 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
## 847 GO:2000116 8.387677e-04 4.436932 1.9997520 8 96 regulation of cysteine-type endopeptidase activity
## 856 GO:0019886 3.904414e-03 4.357807 1.5123122 6 71 antigen processing and presentation of exogenous peptide antigen via MHC class II
## 857 GO:0034340 3.904414e-03 4.357807 1.5123122 6 71 response to type I interferon
## 859 GO:0006919 8.191178e-03 4.351301 1.2567102 5 59 activation of cysteine-type endopeptidase activity involved in apoptotic process
## 903 GO:0032091 9.408953e-03 4.194834 1.2993105 5 61 negative regulation of protein binding
## 904 GO:0032535 1.255250e-05 4.194645 4.0669951 15 192 regulation of cellular component size
## 905 GO:0051179 9.965242e-03 4.168432 1.3240475 5 101 localization
## 907 GO:0055086 1.377714e-06 4.125007 5.3378241 19 253 nucleobase-containing small molecule metabolic process
## 908 GO:0009144 4.467631e-06 4.124412 4.7218935 17 224 purine nucleoside triphosphate metabolic process
## 910 GO:1902903 7.181027e-04 4.081469 2.4370113 9 119 regulation of supramolecular fiber organization
## 912 GO:0031333 5.315472e-03 4.068330 1.6096540 6 76 negative regulation of protein complex assembly
## 919 GO:0009126 6.929305e-06 3.977050 4.8777395 17 229 purine nucleoside monophosphate metabolic process
## 923 GO:0009199 8.244343e-06 3.920036 4.9416400 17 232 ribonucleoside triphosphate metabolic process
## 935 GO:0010959 3.602610e-03 3.851703 1.9826303 7 94 regulation of metal ion transport
## 949 GO:0097237 1.101792e-03 3.823986 2.5871039 9 122 cellular response to toxic substance
## 951 GO:0045087 1.131734e-03 3.810534 2.5980265 9 138 innate immune response
## 953 GO:0034764 7.434926e-03 3.771976 1.7253140 6 81 positive regulation of transmembrane transport
## 954 GO:0009161 1.363719e-05 3.758156 5.1333415 17 241 ribonucleoside monophosphate metabolic process
## 963 GO:0009314 8.043243e-03 3.705628 1.7541829 6 83 response to radiation
## 966 GO:0031145 1.552432e-02 3.666760 1.4697119 5 69 anaphase-promoting complex-dependent catabolic process
## 967 GO:0060071 1.552432e-02 3.666760 1.4697119 5 69 Wnt signaling pathway, planar cell polarity pathway
## 968 GO:0051092 2.611351e-03 3.657343 2.3856193 8 112 positive regulation of NF-kappaB transcription factor activity
## 969 GO:0071222 1.569025e-02 3.655478 1.4735017 5 70 cellular response to lipopolysaccharide
## 970 GO:0050729 1.573462e-02 3.652456 1.4745011 5 70 positive regulation of inflammatory response
## 971 GO:0002793 5.034472e-03 3.606061 2.1063830 7 99 positive regulation of peptide secretion
## 994 GO:0098660 1.034114e-05 3.536029 6.1131495 19 287 inorganic ion transmembrane transport
## 995 GO:0043900 1.774950e-02 3.533297 1.5199093 5 74 regulation of multi-organism process
## 997 GO:0002253 4.018213e-04 3.497592 3.7953424 12 191 activation of immune response
## 999 GO:0080134 3.555800e-07 3.472213 9.2175049 27 441 regulation of response to stress
## 1007 GO:0008360 1.158893e-02 3.404949 1.8957153 6 89 regulation of cell shape
## 1008 GO:0016310 8.689210e-04 3.398428 3.5799714 11 184 phosphorylation
## 1011 GO:0001736 2.154829e-02 3.349915 1.5975129 5 75 establishment of planar polarity
## 1049 GO:0033209 2.334866e-02 3.274724 1.6308301 5 78 tumor necrosis factor-mediated signaling pathway
## 1050 GO:0002695 1.385619e-02 3.264645 1.9706788 6 93 negative regulation of leukocyte activation
## 1051 GO:0060759 2.375957e-02 3.259731 1.6385006 5 77 regulation of response to cytokine stimulus
## 1056 GO:0045861 3.348514e-03 3.208230 3.0392496 9 144 negative regulation of proteolysis
## 1057 GO:0071216 5.477112e-03 3.205985 2.6928008 8 127 cellular response to biotic stimulus
## 1058 GO:0098609 1.497295e-02 3.205330 2.0045738 6 98 cell-cell adhesion
## 1059 GO:0010639 5.507338e-03 3.203313 2.6955763 8 128 negative regulation of organelle organization
## 1061 GO:0045088 3.665984e-04 3.166529 4.8828717 14 234 regulation of innate immune response
## 1070 GO:0008637 2.840499e-02 3.098802 1.7170323 5 81 apoptotic mitochondrial changes
## 1076 GO:0071241 1.757975e-02 3.084468 2.0771411 6 98 cellular response to inorganic substance
## 1087 GO:0002764 1.824185e-02 3.056970 2.0943613 6 105 immune response-regulating signaling pathway
## 1090 GO:0051224 1.880258e-02 3.034962 2.1087171 6 99 negative regulation of protein transport
## 1091 GO:0010638 3.605148e-04 3.034532 5.4666500 15 268 positive regulation of organelle organization
## 1092 GO:0034097 1.675187e-04 3.031842 6.2878945 17 333 response to cytokine
## 1094 GO:0009259 7.145530e-05 3.031737 7.0277743 19 331 ribonucleotide metabolic process
## 1095 GO:0070838 1.285248e-03 3.027414 4.3239350 12 203 divalent metal ion transport
## 1096 GO:0002758 1.340708e-03 3.011258 4.3452352 12 204 innate immune response-activating signal transduction
## 1097 GO:0006163 1.731467e-04 3.009462 6.2848643 17 300 purine nucleotide metabolic process
## 1099 GO:0043207 4.290095e-06 2.990059 10.4370845 27 490 response to external biotic stimulus
## 1103 GO:0002223 3.314077e-02 2.964888 1.7892145 5 84 stimulatory C-type lectin receptor signaling pathway
## 1104 GO:0070374 3.314077e-02 2.964888 1.7892145 5 84 positive regulation of ERK1 and ERK2 cascade
## 1108 GO:0098657 3.134935e-05 2.957255 8.4224063 22 396 import into cell
## 1111 GO:0038095 2.145763e-02 2.938997 2.1726176 6 102 Fc-epsilon receptor signaling pathway
## 1113 GO:0090263 3.462784e-02 2.927455 1.8105147 5 85 positive regulation of canonical Wnt signaling pathway
## 1145 GO:0055082 9.853231e-05 2.863762 7.8171633 20 367 cellular chemical homeostasis
## 1146 GO:0045862 1.378459e-03 2.854460 4.9629402 13 233 positive regulation of proteolysis
## 1149 GO:0051090 7.140898e-03 2.829779 3.4141414 9 162 regulation of DNA-binding transcription factor activity
## 1157 GO:1903532 5.635621e-03 2.757545 3.8979315 10 183 positive regulation of secretion by cell
## 1159 GO:0051607 2.799423e-02 2.751986 2.3099517 6 109 defense response to virus
## 1164 GO:0051222 1.911779e-02 2.734618 2.7210434 7 129 positive regulation of protein transport
## 1168 GO:1905330 4.441418e-02 2.721138 1.9383157 5 91 regulation of morphogenesis of an epithelium
## 1193 GO:0043123 2.030919e-02 2.698251 2.7543730 7 130 positive regulation of I-kappaB kinase/NF-kappaB signaling
## 1194 GO:0098655 9.699322e-03 2.684874 3.5851463 9 177 cation transmembrane transport
## 1198 GO:0032879 3.552854e-03 2.667857 4.9033347 12 264 regulation of localization
## 1199 GO:0033002 4.800924e-02 2.658617 1.9809160 5 93 muscle cell proliferation
## 1201 GO:0044089 5.030226e-03 2.654528 4.4592243 11 211 positive regulation of cellular component biogenesis
## 1213 GO:0031349 4.031702e-03 2.609037 4.9627144 12 242 positive regulation of defense response
## 1243 GO:0010942 7.061692e-04 2.557989 7.7447839 18 369 positive regulation of cell death
## 1255 GO:0050708 8.261426e-03 2.466122 4.7712386 11 224 regulation of protein secretion
## 1257 GO:0051046 1.396636e-03 2.461462 7.5402610 17 354 regulation of secretion
## 1259 GO:0090087 8.076983e-04 2.457468 8.4987688 19 399 regulation of peptide transport
## 1263 GO:0070201 3.150466e-02 2.447226 3.0192528 7 148 regulation of establishment of protein localization
## 1270 GO:0060341 2.302138e-02 2.439048 3.4747397 8 170 regulation of cellular localization
## 1293 GO:0051346 1.288988e-02 2.414126 4.4091357 10 207 negative regulation of hydrolase activity
## 1295 GO:0043488 3.394986e-02 2.404538 3.0672248 7 144 regulation of mRNA stability
## 1297 GO:0009617 1.808260e-02 2.402354 3.9751151 9 196 response to bacterium
## 1300 GO:0050821 4.882589e-02 2.384350 2.6412214 6 124 protein stabilization
## 1306 GO:0065008 6.729104e-03 2.367629 6.0199637 13 372 regulation of biological quality
## 1307 GO:0061024 2.697872e-02 2.361309 3.5813775 8 179 membrane organization
## 1312 GO:0051098 1.159606e-02 2.341683 5.0055405 11 235 regulation of binding
## 1315 GO:0022610 3.412907e-04 2.326874 11.9919970 25 563 biological adhesion
## 1322 GO:0055085 3.453336e-03 2.306595 7.5342413 16 377 transmembrane transport
## 1346 GO:0060627 3.233094e-02 2.272781 3.7081930 8 177 regulation of vesicle-mediated transport
## 1355 GO:0043086 2.698324e-02 2.229634 4.2629185 9 207 negative regulation of catalytic activity
## 1358 GO:0032268 2.208602e-02 2.213115 4.8160371 10 254 regulation of cellular protein metabolic process
## 1366 GO:0009611 2.909536e-02 2.196902 4.3198607 9 208 response to wounding
## 1367 GO:0002521 4.995060e-02 2.196135 3.3404202 7 159 leukocyte differentiation
## 1380 GO:0000165 3.888420e-02 2.186439 3.8475399 8 187 MAPK cascade
## 1424 GO:0032870 4.172505e-02 2.046631 4.6157320 9 219 cellular response to hormone stimulus
##
## $Monocyte$up
## GOBPID Pvalue OddsRatio ExpCount Count Size Term
## 299 GO:0061844 1.669890e-05 20.967230 0.3486826 5 16 antimicrobial humoral immune response mediated by antimicrobial peptide
## 491 GO:0009409 3.038636e-04 10.012639 0.6101945 5 28 response to cold
## 492 GO:0061045 3.038636e-04 10.012639 0.6101945 5 28 negative regulation of wound healing
## 642 GO:1990868 3.070875e-04 7.499289 0.9370845 6 43 response to chemokine
## 646 GO:0071222 1.710086e-05 7.011326 1.5081724 9 70 cellular response to lipopolysaccharide
## 661 GO:0006959 1.659172e-04 6.830729 1.1894464 7 55 humoral immune response
## 662 GO:0002576 6.048645e-05 6.790748 1.3729377 8 63 platelet degranulation
## 720 GO:0046545 1.843451e-03 6.386466 0.8934991 5 41 development of primary female sexual characteristics
## 724 GO:0071456 3.072604e-04 6.110553 1.3106061 7 61 cellular response to hypoxia
## 730 GO:1903034 1.582321e-04 5.829142 1.5690717 8 72 regulation of response to wounding
## 795 GO:0048661 3.089279e-03 5.604084 1.0024624 5 46 positive regulation of smooth muscle cell proliferation
## 809 GO:0033002 7.048687e-04 5.251002 1.4996295 7 69 muscle cell proliferation
## 811 GO:0030278 3.600356e-04 5.104645 1.7652056 8 81 regulation of ossification
## 812 GO:0019935 4.452788e-03 5.103359 1.0896331 5 50 cyclic-nucleotide-mediated signaling
## 875 GO:0045766 1.144730e-03 4.797424 1.6256158 7 75 positive regulation of angiogenesis
## 888 GO:0071216 3.131718e-05 4.690724 2.9047912 12 134 cellular response to biotic stimulus
## 889 GO:0050900 2.814765e-03 4.680847 1.4168445 6 68 leukocyte migration
## 897 GO:0010594 1.489024e-03 4.566529 1.6998276 7 78 regulation of endothelial cell migration
## 940 GO:0006757 1.855734e-03 4.379730 1.7652056 7 81 ATP generation from ADP
## 941 GO:0042866 1.855734e-03 4.379730 1.7652056 7 81 pyruvate biosynthetic process
## 943 GO:0072525 9.456256e-04 4.351606 2.0371875 8 94 pyridine-containing compound biosynthetic process
## 947 GO:0009166 9.996479e-04 4.311377 2.0544983 8 95 nucleotide catabolic process
## 948 GO:0046939 1.050937e-03 4.275590 2.0703029 8 95 nucleotide phosphorylation
## 950 GO:0009179 1.125555e-03 4.226466 2.0920955 8 96 purine ribonucleoside diphosphate metabolic process
## 952 GO:0042107 9.476212e-03 4.189261 1.3019356 5 60 cytokine metabolic process
## 995 GO:0070482 3.259791e-06 4.031649 5.1212755 18 235 response to oxygen levels
## 997 GO:0014070 3.018270e-03 3.989070 1.9218569 7 92 response to organic cyclic compound
## 1006 GO:0097529 3.505360e-03 3.873767 1.9733859 7 91 myeloid leukocyte migration
## 1010 GO:0009617 6.250199e-05 3.806653 4.1286870 14 194 response to bacterium
## 1039 GO:0072599 2.396349e-03 3.713609 2.3536075 8 108 establishment of protein localization to endoplasmic reticulum
## 1044 GO:0034404 1.420596e-03 3.677318 2.6823239 9 124 nucleobase-containing small molecule biosynthetic process
## 1045 GO:0009132 2.539100e-03 3.676372 2.3754001 8 109 nucleoside diphosphate metabolic process
## 1051 GO:0019362 1.583023e-03 3.615610 2.7240827 9 125 pyridine nucleotide metabolic process
## 1052 GO:0006754 5.128679e-03 3.593791 2.1138882 7 97 ATP biosynthetic process
## 1053 GO:0046434 5.502637e-04 3.589818 3.3778626 11 155 organophosphate catabolic process
## 1061 GO:0008285 7.151366e-05 3.561952 4.7196110 15 224 negative regulation of cell proliferation
## 1062 GO:0007423 1.740010e-02 3.554673 1.5127087 5 71 sensory organ development
## 1064 GO:0010634 1.764158e-02 3.542060 1.5181762 5 70 positive regulation of epithelial cell migration
## 1065 GO:0001568 4.669190e-05 3.532121 5.0890979 16 235 blood vessel development
## 1084 GO:0007568 4.229776e-04 3.472170 3.8137158 12 175 aging
## 1111 GO:0150063 4.145092e-03 3.371705 2.5715341 8 118 visual system development
## 1117 GO:0051897 2.233073e-02 3.318166 1.6126570 5 74 positive regulation of protein kinase B signaling
## 1120 GO:0072358 2.441932e-05 3.304160 6.4942132 19 298 cardiovascular system development
## 1121 GO:0001659 1.321439e-02 3.302521 1.9507389 6 90 temperature homeostasis
## 1124 GO:2000116 1.830475e-03 3.267032 3.3342773 10 153 regulation of cysteine-type endopeptidase activity
## 1127 GO:0009145 8.269014e-03 3.263339 2.3100222 7 106 purine nucleoside triphosphate biosynthetic process
## 1148 GO:0090130 3.600993e-03 3.170860 3.0727653 9 141 tissue migration
## 1149 GO:0006614 1.572474e-02 3.169187 2.0267176 6 93 SRP-dependent cotranslational protein targeting to membrane
## 1152 GO:0001666 2.631348e-02 3.166476 1.6826430 5 81 response to hypoxia
## 1153 GO:0010951 1.610715e-02 3.150802 2.0374384 6 94 negative regulation of endopeptidase activity
## 1158 GO:0009201 1.004606e-02 3.135009 2.3971928 7 110 ribonucleoside triphosphate biosynthetic process
## 1184 GO:0040011 3.242637e-03 3.007716 3.6101155 10 185 locomotion
## 1211 GO:0030334 8.198351e-03 2.978577 2.8847721 8 139 regulation of cell migration
## 1214 GO:1903707 3.296757e-02 2.970402 1.7869983 5 82 negative regulation of hemopoiesis
## 1219 GO:0000184 1.321305e-02 2.960173 2.5279488 7 116 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
## 1220 GO:0009127 1.321305e-02 2.960173 2.5279488 7 116 purine nucleoside monophosphate biosynthetic process
## 1223 GO:1990845 3.448502e-02 2.931947 1.8087909 5 83 adaptive thermogenesis
## 1224 GO:0007548 2.173407e-02 2.930571 2.1792662 6 100 sex differentiation
## 1231 GO:0009156 1.469929e-02 2.893861 2.5815358 7 119 ribonucleoside monophosphate biosynthetic process
## 1235 GO:0052547 2.001816e-03 2.860310 4.5550900 12 210 regulation of peptidase activity
## 1273 GO:0008406 4.098426e-02 2.787507 1.8959616 5 87 gonad development
## 1274 GO:0009607 5.786263e-04 2.782592 6.3388889 16 308 response to biotic stimulus
## 1278 GO:0009605 3.248673e-04 2.765683 7.2909066 18 380 response to external stimulus
## 1279 GO:1901136 4.224515e-02 2.762629 1.9118627 5 88 carbohydrate derivative catabolic process
## 1284 GO:0034101 4.271742e-02 2.753572 1.9177542 5 88 erythrocyte homeostasis
## 1285 GO:0070498 4.271742e-02 2.753572 1.9177542 5 88 interleukin-1-mediated signaling pathway
## 1289 GO:0035239 4.053491e-03 2.738875 4.3333333 11 205 tube morphogenesis
## 1294 GO:0006874 9.681732e-03 2.684938 3.5834156 9 165 cellular calcium ion homeostasis
## 1296 GO:0006413 3.111959e-02 2.680301 2.3683884 6 109 translational initiation
## 1330 GO:0044057 7.646766e-03 2.627964 4.0752278 10 187 regulation of system process
## 1331 GO:0009719 3.406146e-02 2.621622 2.4207981 6 117 response to endogenous stimulus
## 1332 GO:0051347 8.402628e-04 2.588852 7.1983195 17 331 positive regulation of transferase activity
## 1339 GO:0070663 2.598953e-02 2.555229 2.8984240 7 133 regulation of leukocyte proliferation
## 1341 GO:0010950 3.802713e-02 2.546134 2.4843635 6 114 positive regulation of endopeptidase activity
## 1343 GO:0008284 2.577326e-03 2.542912 5.9744617 14 291 positive regulation of cell proliferation
## 1345 GO:0043123 2.693633e-02 2.534785 2.9202167 7 134 positive regulation of I-kappaB kinase/NF-kappaB signaling
## 1346 GO:0042330 3.727544e-03 2.523156 5.5571288 13 255 taxis
## 1369 GO:0060759 4.085424e-02 2.499203 2.5279488 6 116 regulation of response to cytokine stimulus
## 1371 GO:0046394 5.742256e-03 2.483990 5.1866535 12 238 carboxylic acid biosynthetic process
## 1373 GO:0001655 4.231645e-02 2.476371 2.5497414 6 117 urogenital system development
## 1374 GO:0002793 2.991734e-02 2.475339 2.9855947 7 137 positive regulation of peptide secretion
## 1376 GO:0006954 2.171167e-02 2.467259 3.4359136 8 169 inflammatory response
## 1381 GO:0006479 4.381130e-02 2.453947 2.5715341 6 118 protein methylation
## 1382 GO:0009108 1.620266e-02 2.450105 3.9008865 9 179 coenzyme biosynthetic process
## 1425 GO:0072507 1.540644e-02 2.342890 4.5328737 10 208 divalent inorganic cation homeostasis
## 1427 GO:1901137 1.188845e-02 2.333897 5.0252653 11 234 carbohydrate derivative biosynthetic process
## 1428 GO:0051094 9.088891e-03 2.332031 5.5122766 12 268 positive regulation of developmental process
## 1429 GO:0010942 2.381001e-03 2.330256 7.9280924 17 369 positive regulation of cell death
## 1430 GO:0009260 2.885093e-02 2.327044 3.6264035 8 167 ribonucleotide biosynthetic process
## 1433 GO:0000122 7.328407e-04 2.314878 10.4822704 22 481 negative regulation of transcription by RNA polymerase II
## 1453 GO:0006402 4.478501e-02 2.254402 3.2596407 7 150 mRNA catabolic process
## 1470 GO:0042060 4.506747e-02 2.250531 3.2638128 7 158 wound healing
## 1472 GO:0051222 1.525256e-02 2.242840 5.2084462 11 239 positive regulation of protein transport
## 1473 GO:0045937 1.379138e-03 2.237917 10.2911345 21 477 positive regulation of phosphate metabolic process
## 1474 GO:1901698 4.743609e-04 2.232056 12.9666338 26 595 response to nitrogen compound
## 1475 GO:0055082 9.521171e-03 2.229746 6.2305110 13 288 cellular chemical homeostasis
## 1481 GO:0045785 2.379268e-02 2.173742 4.8599606 10 224 positive regulation of cell adhesion
## 1485 GO:0034655 2.407973e-03 2.169441 10.0467359 20 467 nucleobase-containing compound catabolic process
## 1488 GO:0045944 8.909530e-04 2.162663 12.7956989 25 595 positive regulation of transcription by RNA polymerase II
## 1491 GO:0002694 1.227915e-02 2.151965 6.4355775 13 296 regulation of leukocyte activation
## 1493 GO:0034248 1.237976e-02 2.149739 6.4428536 13 300 regulation of cellular amide metabolic process
## 1511 GO:0061458 4.292824e-02 2.138728 3.9236359 8 181 reproductive system development
## 1516 GO:0035556 1.404675e-02 2.123808 6.5748876 13 331 intracellular signal transduction
## 1520 GO:0032101 9.141428e-03 2.109210 7.6128554 15 356 regulation of response to external stimulus
## 1521 GO:0044703 1.779835e-02 2.108611 6.0380929 12 282 multi-organism reproductive process
## 1532 GO:0043900 2.443010e-02 2.077463 5.5921182 11 258 regulation of multi-organism process
## 1535 GO:0032270 2.709855e-03 2.072438 11.6301616 22 553 positive regulation of cellular protein metabolic process
##
##
## $T
## $T$down
## GOBPID Pvalue OddsRatio ExpCount Count Size Term
## 110 GO:0034314 7.982351e-06 25.597545 0.3055110 5 14 Arp2/3 complex-mediated actin nucleation
## 166 GO:0001916 1.763484e-05 20.721003 0.3526225 5 16 positive regulation of T cell mediated cytotoxicity
## 236 GO:0034113 1.171800e-04 12.715157 0.5044978 5 23 heterotypic cell-cell adhesion
## 292 GO:0002252 1.255925e-08 10.707899 1.4224628 12 73 immune effector process
## 293 GO:0038093 3.024638e-07 10.181438 1.2295511 10 57 Fc receptor signaling pathway
## 307 GO:0002479 2.255943e-07 9.058688 1.4986457 11 68 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent
## 347 GO:0008064 2.898117e-09 8.661475 2.1598129 15 98 regulation of actin polymerization or depolymerization
## 356 GO:0035722 2.169621e-04 8.067664 0.8815563 6 40 interleukin-12-mediated signaling pathway
## 360 GO:0038096 7.149149e-06 7.923858 1.3596156 9 62 Fc-gamma receptor signaling pathway involved in phagocytosis
## 363 GO:0070527 9.333728e-04 7.579502 0.7713617 5 35 platelet aggregation
## 414 GO:0070671 3.262490e-04 7.410717 0.9476730 6 43 response to interleukin-12
## 415 GO:0048013 1.146508e-04 7.306158 1.1239842 7 51 ephrin receptor signaling pathway
## 416 GO:0002478 1.279356e-05 7.305256 1.4568837 9 67 antigen processing and presentation of exogenous peptide antigen
## 419 GO:0098609 5.555934e-05 6.869506 1.3555300 8 66 cell-cell adhesion
## 421 GO:0002709 5.342335e-04 6.684337 1.0358286 6 47 regulation of T cell mediated immunity
## 464 GO:0060337 1.917364e-03 6.327071 0.9015442 5 41 type I interferon signaling pathway
## 465 GO:0031343 1.936865e-03 6.311462 0.9035952 5 41 positive regulation of cell killing
## 466 GO:0032677 1.936865e-03 6.311462 0.9035952 5 41 regulation of interleukin-8 production
## 468 GO:0006521 7.486214e-04 6.226222 1.1019453 6 50 regulation of cellular amino acid metabolic process
## 469 GO:0006955 1.106317e-04 6.154548 1.4898517 8 90 immune response
## 471 GO:0032271 4.557132e-07 6.098193 2.7107855 14 123 regulation of protein polymerization
## 472 GO:0002824 2.374735e-03 5.994068 0.9452884 5 43 positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
## 473 GO:0006909 8.406160e-06 5.978645 2.1369114 11 100 phagocytosis
## 476 GO:0032956 3.456776e-06 5.968558 2.3466600 12 108 regulation of actin cytoskeleton organization
## 482 GO:0038061 1.049989e-03 5.792899 1.1731844 6 54 NIK/NF-kappaB signaling
## 483 GO:0071346 2.768479e-03 5.762500 0.9780179 5 45 cellular response to interferon-gamma
## 484 GO:0045454 1.131431e-03 5.704480 1.1901010 6 54 cell redox homeostasis
## 487 GO:0002474 1.972866e-04 5.624810 1.6185720 8 75 antigen processing and presentation of peptide antigen via MHC class I
## 517 GO:0033209 2.651865e-04 5.363901 1.6887294 8 78 tumor necrosis factor-mediated signaling pathway
## 518 GO:0001906 3.873261e-03 5.287117 1.0550674 5 49 cell killing
## 525 GO:0031145 7.658134e-04 5.173200 1.5206846 7 69 anaphase-promoting complex-dependent catabolic process
## 526 GO:0009308 8.145698e-04 5.113710 1.5361854 7 70 amine metabolic process
## 561 GO:0019882 4.460448e-04 4.928096 1.8211261 8 85 antigen processing and presentation
## 568 GO:0032535 9.153550e-07 4.686389 4.2088670 17 192 regulation of cellular component size
## 572 GO:0071897 6.954720e-03 4.547674 1.2094670 5 55 DNA biosynthetic process
## 574 GO:0002253 2.887394e-06 4.515854 4.0854322 16 191 activation of immune response
## 576 GO:0060402 3.454560e-03 4.481380 1.4766067 6 67 calcium ion transport into cytosol
## 585 GO:0010950 1.974258e-04 4.460059 2.5124354 10 114 positive regulation of endopeptidase activity
## 607 GO:0050852 1.139607e-04 4.379110 2.8213271 11 129 T cell receptor signaling pathway
## 610 GO:0010972 4.002489e-03 4.338013 1.5206846 6 69 negative regulation of G2/M transition of mitotic cell cycle
## 611 GO:0060071 4.002489e-03 4.338013 1.5206846 6 69 Wnt signaling pathway, planar cell polarity pathway
## 612 GO:0050900 8.459762e-03 4.314557 1.2664908 5 60 leukocyte migration
## 617 GO:0031334 1.439035e-04 4.254645 2.8955962 11 133 positive regulation of protein complex assembly
## 618 GO:0002429 1.574128e-07 4.224703 6.1047771 22 277 immune response-activating cell surface receptor signaling pathway
## 621 GO:0034340 4.612298e-03 4.203468 1.5647624 6 71 response to type I interferon
## 624 GO:0002223 2.438965e-03 4.157505 1.8512682 7 84 stimulatory C-type lectin receptor signaling pathway
## 631 GO:0031146 5.287992e-03 4.076956 1.6088402 6 73 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
## 658 GO:1902036 1.080495e-02 4.047106 1.3443733 5 61 regulation of hematopoietic stem cell differentiation
## 663 GO:0001736 6.033583e-03 3.957778 1.6529180 6 75 establishment of planar polarity
## 665 GO:1902903 9.664640e-04 3.902677 2.5403997 9 119 regulation of supramolecular fiber organization
## 666 GO:0042773 6.433842e-03 3.900743 1.6749569 6 76 ATP synthesis coupled electron transport
## 671 GO:0045862 3.059441e-04 3.871679 3.1549857 11 144 positive regulation of proteolysis
## 672 GO:0048584 6.169618e-06 3.867143 5.3934128 18 271 positive regulation of response to stimulus
## 675 GO:0046034 3.761076e-03 3.821768 1.9987514 7 92 ATP metabolic process
## 676 GO:0070588 2.104939e-03 3.798666 2.3059840 8 105 calcium ion transmembrane transport
## 677 GO:0002703 6.436540e-04 3.793287 2.9091357 10 132 regulation of leukocyte mediated immunity
## 690 GO:0051260 2.352707e-03 3.725988 2.3469514 8 108 protein homooligomerization
## 707 GO:0009199 1.354363e-03 3.705939 2.6647529 9 122 ribonucleoside triphosphate metabolic process
## 712 GO:0061418 1.579071e-02 3.652670 1.4766067 5 67 regulation of transcription from RNA polymerase II promoter in response to hypoxia
## 716 GO:0034612 1.817623e-04 3.602410 4.0110810 13 182 response to tumor necrosis factor
## 723 GO:0022900 1.711083e-03 3.572160 2.7548633 9 125 electron transport chain
## 726 GO:1903555 5.450008e-03 3.551098 2.1377739 7 97 regulation of tumor necrosis factor superfamily cytokine production
## 729 GO:0009144 1.887128e-03 3.518174 2.7944112 9 128 purine nucleoside triphosphate metabolic process
## 734 GO:0002684 1.490400e-05 3.449700 6.2898364 19 313 positive regulation of immune system process
## 754 GO:0070498 1.285697e-02 3.324827 1.9394238 6 88 interleukin-1-mediated signaling pathway
## 756 GO:0050776 7.800158e-03 3.303153 2.2850744 7 118 regulation of immune response
## 762 GO:0044409 2.454444e-02 3.231938 1.6529180 5 75 entry into host
## 763 GO:0051806 2.454444e-02 3.231938 1.6529180 5 75 entry into cell of other organism involved in symbiotic interaction
## 764 GO:2000116 1.989528e-03 3.227542 3.3719527 10 153 regulation of cysteine-type endopeptidase activity
## 765 GO:0052547 3.124754e-04 3.218835 4.8044817 14 218 regulation of peptidase activity
## 766 GO:0043312 6.186688e-06 3.218304 8.1776081 23 373 neutrophil degranulation
## 768 GO:0055074 8.076990e-04 3.208342 4.0992366 12 186 calcium ion homeostasis
## 770 GO:1905330 1.498702e-02 3.206256 2.0055405 6 91 regulation of morphogenesis of an epithelium
## 772 GO:1903706 9.110559e-03 3.199415 2.3530599 7 111 regulation of hemopoiesis
## 774 GO:0042119 6.856282e-06 3.196224 8.2285503 23 375 neutrophil activation
## 791 GO:0060759 2.705328e-02 3.144268 1.6956576 5 77 regulation of response to cytokine stimulus
## 792 GO:0043900 6.123010e-03 3.143149 2.7446169 8 126 regulation of multi-organism process
## 795 GO:2000027 1.064701e-02 3.097765 2.4242797 7 110 regulation of animal organ morphogenesis
## 796 GO:0042180 4.257376e-03 3.085206 3.1515637 9 143 cellular ketone metabolic process
## 799 GO:1903039 4.337708e-03 3.075740 3.1605425 9 144 positive regulation of leukocyte cell-cell adhesion
## 801 GO:0002244 1.115844e-02 3.067587 2.4463186 7 111 hematopoietic progenitor cell differentiation
## 802 GO:0002764 8.620124e-06 3.064753 8.9477961 24 406 immune response-regulating signaling pathway
## 803 GO:0002444 1.980996e-05 3.054634 8.1713507 22 375 myeloid leukocyte mediated immunity
## 804 GO:0002275 2.026063e-05 3.049637 8.1830098 22 376 myeloid cell activation involved in immune response
## 809 GO:0006875 4.140058e-04 2.986901 5.5317656 15 251 cellular metal ion homeostasis
## 811 GO:0051235 2.238759e-03 2.975912 4.0110810 11 182 maintenance of location
## 827 GO:0072503 2.279572e-03 2.968667 4.0204888 11 183 cellular divalent inorganic cation homeostasis
## 828 GO:0009259 3.768489e-03 2.935320 3.6825397 10 168 ribonucleotide metabolic process
## 830 GO:0002263 3.216358e-06 2.915263 11.5263482 29 523 cell activation involved in immune response
## 832 GO:0051250 3.593611e-02 2.897510 1.8292293 5 83 negative regulation of lymphocyte activation
## 833 GO:0043620 2.282418e-02 2.895954 2.2038907 6 100 regulation of DNA-templated transcription in response to stress
## 834 GO:0006887 1.189376e-05 2.868337 10.3839442 26 476 exocytosis
## 835 GO:0046649 2.398318e-02 2.861005 2.2291667 6 107 lymphocyte activation
## 837 GO:0006163 4.630907e-03 2.844157 3.7911839 10 173 purine nucleotide metabolic process
## 838 GO:0098657 5.335146e-05 2.841252 8.7162112 22 396 import into cell
## 839 GO:0038095 2.488033e-02 2.834899 2.2479685 6 102 Fc-epsilon receptor signaling pathway
## 841 GO:0090263 3.921768e-02 2.824353 1.8733071 5 85 positive regulation of canonical Wnt signaling pathway
## 847 GO:0009126 1.606133e-03 2.801512 5.0469096 13 229 purine nucleoside monophosphate metabolic process
## 853 GO:0032946 4.092488e-02 2.789130 1.8953460 5 86 positive regulation of mononuclear cell proliferation
## 885 GO:0060485 4.447294e-02 2.721230 1.9394238 5 88 mesenchyme development
## 886 GO:0007596 1.959720e-02 2.720090 2.7348578 7 125 blood coagulation
## 888 GO:0050792 4.494414e-02 2.712684 1.9451136 5 89 regulation of viral process
## 894 GO:0061024 1.147556e-03 2.684854 6.1098456 15 284 membrane organization
## 897 GO:0050865 4.509303e-04 2.663315 7.4491505 18 338 regulation of cell activation
## 899 GO:0002521 1.505740e-02 2.652756 3.2115869 8 150 leukocyte differentiation
## 900 GO:0009161 2.525007e-03 2.649942 5.3113765 13 241 ribonucleoside monophosphate metabolic process
## 902 GO:0098771 6.698371e-04 2.645968 7.0524501 17 320 inorganic ion homeostasis
## 907 GO:0048863 4.971635e-02 2.631579 2.0007414 5 92 stem cell differentiation
## 932 GO:0045321 7.871821e-04 2.615722 7.1768556 17 356 leukocyte activation
## 933 GO:0030029 1.651975e-02 2.604921 3.2661290 8 160 actin filament-based process
## 936 GO:0071453 1.702949e-02 2.588694 3.2837971 8 149 cellular response to oxygen levels
## 940 GO:0098660 1.635568e-03 2.579470 6.3251662 15 287 inorganic ion transmembrane transport
## 941 GO:0022610 3.680986e-05 2.567605 12.4079045 28 563 biological adhesion
## 942 GO:0097190 3.693089e-02 2.566429 2.4674330 6 115 apoptotic signaling pathway
## 946 GO:0051251 9.180579e-03 2.551940 4.1873923 10 190 positive regulation of lymphocyte activation
## 947 GO:1902749 1.830996e-02 2.551834 3.3278749 8 151 regulation of cell cycle G2/M phase transition
## 969 GO:0071222 4.276993e-02 2.469679 2.5565132 6 116 cellular response to lipopolysaccharide
## 976 GO:0022407 6.477803e-03 2.442481 5.2672987 12 239 regulation of cell-cell adhesion
## 977 GO:0019221 3.354479e-02 2.412528 3.0602873 7 158 cytokine-mediated signaling pathway
## 979 GO:0070838 1.416878e-02 2.376062 4.4738981 10 203 divalent metal ion transport
## 1002 GO:0043488 3.970509e-02 2.318876 3.1736026 7 144 regulation of mRNA stability
## 1004 GO:0001667 2.967815e-02 2.313393 3.6463189 8 168 ameboidal-type cell migration
## 1005 GO:0051047 2.235210e-02 2.308982 4.1221976 9 188 positive regulation of secretion
## 1008 GO:0000902 4.103956e-02 2.302147 3.1976967 7 147 cell morphogenesis
## 1010 GO:0032880 1.339739e-02 2.291395 5.1137678 11 234 regulation of protein localization
## 1018 GO:0062012 4.238920e-02 2.283929 3.2200526 7 147 regulation of small molecule metabolic process
## 1020 GO:0055082 2.948610e-03 2.276561 8.0882787 17 367 cellular chemical homeostasis
## 1021 GO:1901988 3.210031e-02 2.275731 3.7025363 8 168 negative regulation of cell cycle phase transition
## 1023 GO:0060341 3.259127e-02 2.270081 3.7151305 8 170 regulation of cellular localization
## 1032 GO:0050878 3.495348e-02 2.235337 3.7653023 8 174 regulation of body fluid levels
## 1037 GO:0010638 4.537207e-03 2.230973 7.7345878 16 355 positive regulation of organelle organization
## 1058 GO:1903311 4.837026e-02 2.213100 3.3161967 7 151 regulation of mRNA metabolic process
## 1061 GO:0098655 3.798613e-02 2.196450 3.8285821 8 177 cation transmembrane transport
## 1062 GO:0009611 2.970939e-02 2.187793 4.3357819 9 199 response to wounding
## 1067 GO:0060249 2.411989e-02 2.168317 4.8705984 10 221 anatomical structure homeostasis
## 1088 GO:0002758 3.628162e-02 2.103529 4.4959370 9 204 innate immune response-activating signal transduction
## 1090 GO:0002237 4.909394e-02 2.076658 4.0331199 8 183 response to molecule of bacterial origin
## 1095 GO:1901990 4.922236e-02 2.075910 4.0358034 8 187 regulation of mitotic cell cycle phase transition
## 1100 GO:0031347 3.316872e-02 2.048947 5.1393817 10 240 regulation of defense response
## 1102 GO:0051345 9.475487e-03 2.047209 8.3709677 16 390 positive regulation of hydrolase activity
## 1104 GO:0048534 3.168198e-03 2.038187 11.7590645 22 543 hematopoietic or lymphoid organ development
## 1105 GO:0065008 4.293852e-03 2.037234 11.4000000 21 585 regulation of biological quality
## 1108 GO:0055086 2.255116e-02 2.033182 6.2470261 12 287 nucleobase-containing small molecule metabolic process
## 1110 GO:0051272 2.788066e-02 2.031610 5.7080768 11 259 positive regulation of cellular component movement
## 1132 GO:0048729 4.656267e-02 2.000867 4.7115266 9 215 tissue morphogenesis
##
## $T$up
## GOBPID Pvalue OddsRatio ExpCount Count Size Term
## 129 GO:0006614 3.862499e-26 23.482011 2.0725191 29 93 SRP-dependent cotranslational protein targeting to membrane
## 130 GO:0000027 2.826412e-08 22.904624 0.5348436 8 24 ribosomal large subunit assembly
## 186 GO:0000184 3.429385e-26 20.181208 2.4833703 31 112 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
## 187 GO:0006413 2.948640e-25 19.869170 2.4225230 30 109 translational initiation
## 189 GO:0072599 4.756580e-24 18.987175 2.4067964 29 108 establishment of protein localization to endoplasmic reticulum
## 190 GO:0019083 8.353178e-24 18.523163 2.4501488 29 111 viral transcription
## 192 GO:0006612 2.250494e-22 15.032692 2.9774102 30 134 protein targeting to membrane
## 235 GO:0051591 7.807632e-05 14.116071 0.4666091 5 21 response to cAMP
## 238 GO:0006401 5.453285e-20 11.359833 3.8644408 31 179 RNA catabolic process
## 285 GO:0016071 1.977650e-18 9.056195 5.0607879 33 244 mRNA metabolic process
## 286 GO:1902369 1.259190e-04 9.041143 0.8022655 6 36 negative regulation of RNA catabolic process
## 372 GO:0010629 5.801281e-15 7.216501 5.7903538 31 293 negative regulation of gene expression
## 373 GO:1903313 4.954618e-05 7.015562 1.3371091 8 60 positive regulation of mRNA metabolic process
## 416 GO:0002181 3.883429e-05 6.251435 1.6680641 9 76 cytoplasmic translation
## 457 GO:0042254 1.389625e-03 5.458540 1.2370978 6 57 ribosome biogenesis
## 502 GO:0046700 6.534522e-14 4.781399 11.4545678 42 514 heterocycle catabolic process
## 503 GO:0044270 7.473209e-14 4.759949 11.4991381 42 516 cellular nitrogen compound catabolic process
## 506 GO:0019439 1.113241e-13 4.696673 11.6328491 42 522 aromatic compound catabolic process
## 511 GO:0006518 3.603117e-14 4.615385 12.8555542 45 578 peptide metabolic process
## 512 GO:1901361 2.001101e-13 4.604670 11.8334154 42 531 organic cyclic compound catabolic process
## 516 GO:1903312 7.351293e-03 4.483523 1.2256833 5 55 negative regulation of mRNA metabolic process
## 522 GO:0009615 7.671680e-03 4.433551 1.2381910 5 56 response to virus
## 556 GO:0009416 4.969393e-03 4.135035 1.5888293 6 72 response to light stimulus
## 579 GO:0033365 1.093344e-10 3.965396 12.0200698 38 551 protein localization to organelle
## 582 GO:0019538 2.362115e-09 3.903488 12.0387240 35 558 protein metabolic process
## 589 GO:0090092 3.831394e-03 3.808752 2.0056636 7 90 regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
## 590 GO:0042752 1.373261e-02 3.795262 1.4262497 5 64 regulation of circadian rhythm
## 591 GO:1903844 1.373261e-02 3.795262 1.4262497 5 64 regulation of cellular response to transforming growth factor beta stimulus
## 618 GO:0006397 1.015106e-02 3.514286 1.8434091 6 86 mRNA processing
## 669 GO:0002262 8.406957e-03 3.253229 2.3176557 7 104 myeloid cell homeostasis
## 673 GO:0071559 5.791150e-03 3.174932 2.7187885 8 122 response to transforming growth factor beta
## 674 GO:0042594 1.569191e-02 3.172008 2.0262246 6 91 response to starvation
## 699 GO:2001242 1.842102e-02 3.051633 2.0996419 6 95 regulation of intrinsic apoptotic signaling pathway
## 702 GO:0061013 3.133659e-03 3.016924 3.5879094 10 161 regulation of mRNA catabolic process
## 705 GO:0009057 3.351213e-02 2.954967 1.7945243 5 103 macromolecule catabolic process
## 727 GO:0043487 5.980468e-03 2.915656 3.3204876 9 149 regulation of RNA stability
## 760 GO:0009617 3.941602e-03 2.749105 4.3165360 11 196 response to bacterium
## 770 GO:0042770 4.817803e-02 2.657265 1.9833785 5 89 signal transduction in response to DNA damage
## 772 GO:0071216 2.268635e-02 2.634104 2.8180473 7 127 cellular response to biotic stimulus
## 808 GO:0043207 2.109608e-04 2.452093 10.9197242 24 490 response to external biotic stimulus
## 841 GO:0002683 1.183066e-02 2.334105 5.0195182 11 227 negative regulation of immune system process
## 855 GO:0045861 3.003290e-02 2.307692 3.6547648 8 164 negative regulation of proteolysis
## 857 GO:0006364 2.307242e-02 2.295231 4.1450382 9 186 rRNA processing
## 862 GO:0071495 1.858212e-02 2.272090 4.6730619 10 217 cellular response to endogenous stimulus
## 867 GO:0000122 9.911414e-04 2.255436 10.7191578 22 481 negative regulation of transcription by RNA polymerase II
## 869 GO:2001234 4.582091e-02 2.241667 3.2759173 7 147 negative regulation of apoptotic signaling pathway
## 895 GO:0009895 3.097417e-02 2.169693 4.3678897 9 196 negative regulation of catabolic process
## 896 GO:0070925 1.173537e-02 2.166522 6.3997985 13 292 organelle assembly
## 901 GO:0051094 1.320790e-02 2.131585 6.5001281 13 295 positive regulation of developmental process
##
##
## $NK
## $NK$down
## GOBPID Pvalue OddsRatio ExpCount Count Size Term
## 200 GO:0034314 2.577609e-07 34.763158 0.3055110 6 14 Arp2/3 complex-mediated actin nucleation
## 286 GO:0001916 1.763484e-05 20.721003 0.3526225 5 16 positive regulation of T cell mediated cytotoxicity
## 307 GO:0002252 4.050244e-08 15.824176 0.7531585 9 44 immune effector process
## 323 GO:0031343 3.983090e-07 14.891294 0.7239339 8 33 positive regulation of cell killing
## 389 GO:1903307 1.198382e-04 12.651660 0.5068949 5 23 positive regulation of regulated secretory pathway
## 390 GO:0035722 2.003636e-06 11.565789 0.8815563 8 40 interleukin-12-mediated signaling pathway
## 391 GO:0070527 8.964338e-06 11.504360 0.7713617 7 35 platelet aggregation
## 463 GO:0070671 3.570570e-06 10.570426 0.9476730 8 43 response to interleukin-12
## 467 GO:0038096 7.969003e-08 10.187625 1.3596156 11 62 Fc-gamma receptor signaling pathway involved in phagocytosis
## 468 GO:0006968 7.114581e-05 10.168272 0.7272839 6 33 cellular defense response
## 469 GO:0032535 3.276949e-11 10.137902 2.1674141 17 100 regulation of cellular component size
## 475 GO:0048013 1.375506e-06 9.959244 1.1239842 9 51 ephrin receptor signaling pathway
## 476 GO:0001910 8.045137e-05 9.903509 0.7422299 6 34 regulation of leukocyte mediated cytotoxicity
## 556 GO:0006909 7.290724e-07 7.912120 1.6739320 11 80 phagocytosis
## 558 GO:0098609 2.970652e-06 7.648003 1.5589247 10 76 cell-cell adhesion
## 563 GO:0007229 9.750162e-05 7.518836 1.0961941 7 50 integrin-mediated signaling pathway
## 570 GO:0002708 3.121726e-04 7.475581 0.9399778 6 43 positive regulation of lymphocyte mediated immunity
## 616 GO:0032760 3.999112e-04 7.098516 0.9826055 6 45 positive regulation of tumor necrosis factor production
## 617 GO:0002479 1.614627e-05 7.074377 1.4986457 9 68 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent
## 627 GO:0050777 1.687850e-03 6.532392 0.8765631 5 40 negative regulation of immune response
## 677 GO:0060337 1.917364e-03 6.327071 0.9015442 5 41 type I interferon signaling pathway
## 678 GO:0002253 5.444856e-10 6.311685 4.0854322 21 191 activation of immune response
## 679 GO:0006955 6.862053e-04 6.280495 1.0783437 6 74 immune response
## 681 GO:0050776 1.927652e-03 6.271360 0.8989630 5 49 regulation of immune response
## 683 GO:0002824 2.317068e-03 6.029682 0.9399778 5 43 positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
## 684 GO:0051258 1.548954e-08 6.012594 3.5923418 18 163 protein polymerization
## 685 GO:1903555 8.407633e-06 5.981935 2.1377739 11 97 regulation of tumor necrosis factor superfamily cytokine production
## 697 GO:0045454 1.131431e-03 5.704480 1.1901010 6 54 cell redox homeostasis
## 698 GO:0097581 2.941703e-03 5.677443 0.9917508 5 45 lamellipodium organization
## 741 GO:0006521 3.485808e-03 5.435590 1.0304225 5 47 regulation of cellular amino acid metabolic process
## 743 GO:0002709 3.564990e-03 5.405720 1.0358286 5 47 regulation of T cell mediated immunity
## 749 GO:0031334 2.093736e-06 5.292120 3.0705548 14 142 positive regulation of protein complex assembly
## 755 GO:0002576 1.706704e-03 5.222112 1.2864006 6 59 platelet degranulation
## 756 GO:0044106 4.144488e-03 5.199524 1.0719318 5 49 cellular amine metabolic process
## 761 GO:0098869 4.277870e-03 5.158699 1.0799064 5 49 cellular oxidant detoxification
## 762 GO:0002443 4.301010e-03 5.120523 1.0777501 5 60 leukocyte mediated immunity
## 764 GO:0043312 3.623034e-12 5.087890 8.1776081 33 373 neutrophil degranulation
## 780 GO:0002275 1.771410e-12 4.965972 8.9449440 35 408 myeloid cell activation involved in immune response
## 804 GO:0042119 1.858346e-11 4.884769 8.1823225 32 375 neutrophil activation
## 806 GO:1903900 5.875300e-03 4.751696 1.1623095 5 53 regulation of viral life cycle
## 819 GO:0009615 6.808876e-03 4.570045 1.2030151 5 56 response to virus
## 820 GO:0032091 6.880405e-03 4.559538 1.2062592 5 55 negative regulation of protein binding
## 822 GO:0002444 6.386064e-10 4.541011 7.8179903 29 369 myeloid leukocyte mediated immunity
## 823 GO:0032981 7.020777e-03 4.536207 1.2121399 5 55 mitochondrial respiratory chain complex I assembly
## 864 GO:0002263 1.726379e-12 4.444643 11.5263482 40 523 cell activation involved in immune response
## 865 GO:1901657 3.696821e-03 4.415041 1.4967231 6 68 glycosyl compound metabolic process
## 867 GO:0045055 7.303549e-10 4.396238 8.3929685 30 408 regulated exocytosis
## 868 GO:0002685 8.943513e-04 4.393838 2.0204812 8 92 regulation of leukocyte migration
## 869 GO:0051924 7.968357e-03 4.387299 1.2491024 5 57 regulation of calcium ion transport
## 871 GO:0048525 4.002489e-03 4.338013 1.5206846 6 69 negative regulation of viral process
## 872 GO:0060071 4.002489e-03 4.338013 1.5206846 6 69 Wnt signaling pathway, planar cell polarity pathway
## 876 GO:0043900 2.128190e-03 4.267184 1.8077020 7 84 regulation of multi-organism process
## 881 GO:0019884 8.014101e-05 4.219531 3.1956415 12 145 antigen processing and presentation of exogenous antigen
## 882 GO:0060402 9.241678e-03 4.218583 1.2943061 5 59 calcium ion transport into cytosol
## 884 GO:0048002 8.153717e-05 4.211113 3.2012811 12 146 antigen processing and presentation of peptide antigen
## 886 GO:0034340 4.612298e-03 4.203468 1.5647624 6 71 response to type I interferon
## 888 GO:0098754 9.417587e-03 4.198063 1.3002955 5 59 detoxification
## 890 GO:0007163 6.242855e-04 4.171953 2.3917653 9 109 establishment or maintenance of cell polarity
## 892 GO:0002758 4.925464e-03 4.143316 1.5859825 6 72 innate immune response-activating signal transduction
## 898 GO:0050900 1.050025e-02 4.073060 1.3341705 5 64 leukocyte migration
## 910 GO:0002764 3.665829e-09 4.052013 8.9477961 30 406 immune response-regulating signaling pathway
## 926 GO:0002429 1.874457e-05 4.043940 4.2072307 15 204 immune response-activating cell surface receptor signaling pathway
## 929 GO:0051897 5.651799e-03 4.016491 1.6308791 6 74 positive regulation of protein kinase B signaling
## 930 GO:0098657 8.195315e-09 3.999744 8.7162112 29 396 import into cell
## 934 GO:0001736 6.033583e-03 3.957778 1.6529180 6 75 establishment of planar polarity
## 935 GO:0046649 6.193462e-03 3.930638 1.6609470 6 82 lymphocyte activation
## 937 GO:0008360 3.384773e-03 3.901517 1.9614627 7 89 regulation of cell shape
## 938 GO:0042773 6.433842e-03 3.900743 1.6749569 6 76 ATP synthesis coupled electron transport
## 966 GO:0050852 1.445337e-03 3.667241 2.6888367 9 125 T cell receptor signaling pathway
## 967 GO:0051651 1.579071e-02 3.652670 1.4766067 5 67 maintenance of location in cell
## 976 GO:0022900 1.711083e-03 3.572160 2.7548633 9 125 electron transport chain
## 978 GO:0045580 1.757773e-02 3.546785 1.5170455 5 69 regulation of T cell differentiation
## 981 GO:0031145 1.774441e-02 3.537626 1.5206846 5 69 anaphase-promoting complex-dependent catabolic process
## 983 GO:0002223 1.036043e-02 3.497110 1.8512682 6 84 stimulatory C-type lectin receptor signaling pathway
## 984 GO:0052547 8.818176e-05 3.487324 4.8044817 15 218 regulation of peptidase activity
## 985 GO:1903039 1.171351e-03 3.485119 3.1427867 10 144 positive regulation of leukocyte cell-cell adhesion
## 987 GO:0010950 3.594056e-03 3.458899 2.5124354 8 114 positive regulation of endopeptidase activity
## 1012 GO:0050817 2.239496e-03 3.423302 2.8643607 9 131 coagulation
## 1021 GO:0061572 2.211723e-02 3.327840 1.6088402 5 73 actin filament bundle organization
## 1023 GO:0007599 2.746472e-03 3.313350 2.9514575 9 135 hemostasis
## 1027 GO:0010638 1.158445e-04 3.249544 5.4955519 16 258 positive regulation of organelle organization
## 1029 GO:2000116 1.989528e-03 3.227542 3.3719527 10 153 regulation of cysteine-type endopeptidase activity
## 1031 GO:0051050 5.402824e-03 3.215893 2.6877333 8 133 positive regulation of transport
## 1033 GO:0042060 1.275829e-03 3.213680 3.7391304 11 172 wound healing
## 1038 GO:1905330 1.498702e-02 3.206256 2.0055405 6 91 regulation of morphogenesis of an epithelium
## 1063 GO:0033209 2.722883e-02 3.137867 1.6983793 5 78 tumor necrosis factor-mediated signaling pathway
## 1068 GO:0065008 7.090336e-06 3.092243 9.6051617 25 502 regulation of biological quality
## 1070 GO:0017157 2.911605e-02 3.078039 1.7286085 5 80 regulation of exocytosis
## 1072 GO:0002244 1.115844e-02 3.067587 2.4463186 7 111 hematopoietic progenitor cell differentiation
## 1078 GO:0010951 1.906238e-02 3.026204 2.1157350 6 96 negative regulation of endopeptidase activity
## 1080 GO:0051235 1.929480e-02 3.017081 2.1214232 6 98 maintenance of location
## 1082 GO:0045087 1.222947e-02 3.009736 2.4905072 7 126 innate immune response
## 1083 GO:0046034 1.953810e-02 3.008152 2.1275109 6 98 ATP metabolic process
## 1103 GO:1902105 1.310538e-02 2.965850 2.5241815 7 115 regulation of leukocyte differentiation
## 1104 GO:2000045 3.332731e-02 2.961341 1.7922944 5 82 regulation of G1/S transition of mitotic cell cycle
## 1108 GO:0051224 2.184044e-02 2.927466 2.1818518 6 99 negative regulation of protein transport
## 1110 GO:0001667 3.981159e-03 2.909431 3.7097768 10 170 ameboidal-type cell migration
## 1111 GO:0055074 2.653833e-03 2.906395 4.0992366 11 186 calcium ion homeostasis
## 1113 GO:0030030 3.697259e-02 2.875791 1.8441368 5 85 cell projection organization
## 1118 GO:0070374 3.755483e-02 2.860468 1.8512682 5 84 positive regulation of ERK1 and ERK2 cascade
## 1121 GO:0038095 2.488033e-02 2.834899 2.2479685 6 102 Fc-epsilon receptor signaling pathway
## 1123 GO:0043207 3.386031e-04 2.827786 6.6512155 17 307 response to external biotic stimulus
## 1131 GO:0061024 3.737957e-04 2.802177 6.7091161 17 313 membrane organization
## 1140 GO:0051271 1.157912e-02 2.789875 3.0634080 8 139 negative regulation of cellular component movement
## 1141 GO:0032946 4.092488e-02 2.789130 1.8953460 5 86 positive regulation of mononuclear cell proliferation
## 1142 GO:0001817 4.111978e-02 2.784091 1.8974721 5 93 regulation of cytokine production
## 1161 GO:0001666 2.475590e-03 2.781916 4.6722482 12 212 response to hypoxia
## 1162 GO:0098660 5.744504e-04 2.778892 6.3251662 16 287 inorganic ion transmembrane transport
## 1164 GO:0070588 1.801736e-02 2.770273 2.6887466 7 122 calcium ion transmembrane transport
## 1166 GO:0030336 4.245082e-02 2.758754 1.9144623 5 88 negative regulation of cell migration
## 1168 GO:0090132 1.254853e-02 2.747219 3.1074858 8 141 epithelium migration
## 1170 GO:0051046 2.285639e-04 2.746984 7.6743040 19 350 regulation of secretion
## 1179 GO:0072503 6.973076e-03 2.666873 4.0204888 10 183 cellular divalent inorganic cation homeostasis
## 1181 GO:0051607 3.239078e-02 2.653381 2.3910026 6 109 defense response to virus
## 1191 GO:0040013 1.581497e-02 2.626614 3.2397193 8 147 negative regulation of locomotion
## 1210 GO:2000027 3.433270e-02 2.614162 2.4242797 6 110 regulation of animal organ morphogenesis
## 1215 GO:0030335 1.177446e-02 2.594755 3.6996146 9 172 positive regulation of cell migration
## 1217 GO:0009126 4.631391e-03 2.558349 5.0469096 12 229 purine nucleoside monophosphate metabolic process
## 1221 GO:0006875 3.587033e-03 2.535309 5.5317656 13 251 cellular metal ion homeostasis
## 1222 GO:0009199 5.134189e-03 2.522482 5.1130263 12 232 ribonucleoside triphosphate metabolic process
## 1223 GO:0051251 3.998051e-02 2.513352 2.5147223 6 117 positive regulation of lymphocyte activation
## 1228 GO:0009144 5.492966e-03 2.499110 5.1571042 12 234 purine nucleoside triphosphate metabolic process
## 1230 GO:0051270 1.629538e-03 2.498065 6.9830891 16 326 regulation of cellular component movement
## 1236 GO:0051098 5.679702e-03 2.487581 5.1791431 12 235 regulation of binding
## 1237 GO:0070482 5.679702e-03 2.487581 5.1791431 12 235 response to oxygen levels
## 1257 GO:0060759 4.276993e-02 2.469679 2.5565132 6 116 regulation of response to cytokine stimulus
## 1258 GO:0071222 4.276993e-02 2.469679 2.5565132 6 116 cellular response to lipopolysaccharide
## 1266 GO:0009161 6.908875e-03 2.420521 5.3113765 12 241 ribonucleoside monophosphate metabolic process
## 1270 GO:0036294 3.374241e-02 2.408254 3.0634080 7 139 cellular response to decreased oxygen levels
## 1271 GO:0040012 7.226431e-03 2.407710 5.3461976 12 253 regulation of locomotion
## 1273 GO:0045785 9.812907e-03 2.402342 4.8875740 11 224 positive regulation of cell adhesion
## 1279 GO:0072521 4.188410e-03 2.395435 6.3001867 14 286 purine-containing compound metabolic process
## 1283 GO:0007264 3.484282e-02 2.391291 3.0852537 7 140 small GTPase mediated signal transduction
## 1285 GO:0070838 1.416878e-02 2.376062 4.4738981 10 203 divalent metal ion transport
## 1287 GO:0098771 3.496799e-03 2.366921 6.8444664 15 312 inorganic ion homeostasis
## 1315 GO:0001775 9.901613e-03 2.311401 5.5883212 12 319 cell activation
## 1317 GO:0070201 4.078413e-02 2.305288 3.1931166 7 150 regulation of establishment of protein localization
## 1318 GO:0051130 1.736598e-02 2.299943 4.6247062 10 233 positive regulation of cellular component organization
## 1327 GO:0055082 2.948610e-03 2.276561 8.0882787 17 367 cellular chemical homeostasis
## 1338 GO:0051240 1.191970e-03 2.228533 10.9013401 22 524 positive regulation of multicellular organismal process
## 1360 GO:0090087 2.966891e-03 2.219005 8.7935238 18 399 regulation of peptide transport
## 1363 GO:0042592 5.392836e-04 2.215738 13.0970724 26 600 homeostatic process
## 1375 GO:0060341 2.780636e-03 2.138695 10.1682776 20 461 regulation of cellular localization
## 1379 GO:0007186 4.391635e-02 2.128514 3.9422383 8 182 G protein-coupled receptor signaling pathway
## 1393 GO:0010942 7.599793e-03 2.101397 8.1697902 16 374 positive regulation of cell death
## 1399 GO:0002790 3.184333e-02 2.063300 5.1023573 10 235 peptide secretion
## 1400 GO:0045862 3.308816e-02 2.048452 5.1350653 10 233 positive regulation of proteolysis
## 1422 GO:0019693 1.372826e-02 2.001600 7.9812762 15 364 ribose phosphate metabolic process
##
## $NK$up
## GOBPID Pvalue OddsRatio ExpCount Count Size Term
## 57 GO:0006614 7.310233e-59 69.290981 2.0152672 49 93 SRP-dependent cotranslational protein targeting to membrane
## 58 GO:0019083 1.046886e-55 51.751719 2.3950893 50 111 viral transcription
## 59 GO:0072599 1.269234e-54 51.576538 2.3403103 49 108 establishment of protein localization to endoplasmic reticulum
## 103 GO:0000184 1.090790e-52 45.372077 2.5136666 49 116 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
## 104 GO:0006612 1.408592e-50 37.342857 2.8947044 50 134 protein targeting to membrane
## 108 GO:0006413 1.269785e-44 27.393894 3.4546576 49 160 translational initiation
## 156 GO:0000027 5.049409e-07 19.318830 0.5200689 7 24 ribosomal large subunit assembly
## 205 GO:0002181 1.572191e-13 14.963571 1.5880612 17 74 cytoplasmic translation
## 206 GO:0006401 6.726316e-36 14.775377 5.9004093 52 275 RNA catabolic process
## 262 GO:0019222 4.756282e-18 9.270877 6.5167883 35 372 regulation of metabolic process
## 294 GO:0034097 1.531653e-04 8.645866 0.8280683 6 40 response to cytokine
## 297 GO:1901575 1.789018e-24 8.023189 10.0979303 52 469 organic substance catabolic process
## 300 GO:0006518 2.734918e-27 7.659931 12.4984555 61 578 peptide metabolic process
## 339 GO:0016071 1.152937e-24 7.089018 12.5580235 58 592 mRNA metabolic process
## 427 GO:0006364 1.931213e-07 5.296667 3.7757367 17 175 rRNA processing
## 519 GO:1903313 9.424440e-03 4.195109 1.3001724 5 60 positive regulation of mRNA metabolic process
## 521 GO:0032496 9.510776e-03 4.184058 1.3028978 5 61 response to lipopolysaccharide
## 596 GO:0071826 6.206677e-05 3.608385 4.6589510 15 215 ribonucleoprotein complex subunit organization
## 641 GO:0002262 7.252144e-03 3.351613 2.2536321 7 104 myeloid cell homeostasis
## 643 GO:2001235 7.904819e-03 3.293350 2.2904062 7 106 positive regulation of apoptotic signaling pathway
## 646 GO:0042770 2.384203e-02 3.257249 1.6401529 5 76 signal transduction in response to DNA damage
## 671 GO:0050821 5.404164e-03 3.214286 2.6870229 8 124 protein stabilization
## 701 GO:0017148 3.337144e-02 2.959653 1.7927672 5 83 negative regulation of translation
## 707 GO:0070374 3.530478e-02 2.911763 1.8202413 5 84 positive regulation of ERK1 and ERK2 cascade
## 709 GO:0009617 2.761967e-03 2.891310 4.1214383 11 196 response to bacterium
## 749 GO:0048017 4.538911e-02 2.704162 1.9502586 5 90 inositol lipid-mediated signaling
## 776 GO:0043207 5.030862e-05 2.663605 10.6180744 25 490 response to external biotic stimulus
## 781 GO:0071902 8.195142e-03 2.599063 4.1172125 10 190 positive regulation of protein serine/threonine kinase activity
## 818 GO:0030522 2.245198e-02 2.449642 3.4568115 8 161 intracellular receptor signaling pathway
## 820 GO:0043066 4.873352e-03 2.440438 5.7414906 13 275 negative regulation of apoptotic process
## 838 GO:0045861 2.597650e-02 2.377900 3.5538045 8 164 negative regulation of proteolysis
## 858 GO:0045944 3.853770e-04 2.268452 12.8013589 26 599 positive regulation of transcription by RNA polymerase II
## 885 GO:0034660 2.248810e-03 2.230125 9.2745629 19 428 ncRNA metabolic process
## 909 GO:0060548 4.145299e-03 2.146274 9.0848856 18 430 negative regulation of cell death
## 922 GO:0000122 3.683310e-03 2.081595 10.4230485 20 481 negative regulation of transcription by RNA polymerase II
## 940 GO:0070925 1.235069e-02 2.030903 7.8862701 15 372 organelle assembly
##
##
## $B
## $B$down
## GOBPID Pvalue OddsRatio ExpCount Count Size Term
## 105 GO:0034314 2.250493e-07 35.613772 0.2986068 6 14 Arp2/3 complex-mediated actin nucleation
## 163 GO:0050853 6.061918e-08 20.050729 0.5801432 8 27 B cell receptor signaling pathway
## 217 GO:0035722 1.689926e-06 11.848802 0.8618567 8 40 interleukin-12-mediated signaling pathway
## 260 GO:0070671 3.015507e-06 10.829085 0.9264959 8 43 response to interleukin-12
## 262 GO:0038093 2.430486e-07 10.442928 1.2011222 10 57 Fc receptor signaling pathway
## 263 GO:0032535 2.475623e-11 10.339384 2.1300448 17 100 regulation of cellular component size
## 268 GO:0002252 7.866883e-08 10.128392 1.3516439 11 74 immune effector process
## 318 GO:0048013 1.143241e-05 8.805459 1.0988673 8 51 ephrin receptor signaling pathway
## 320 GO:0002449 4.711954e-05 8.532344 0.9801449 7 47 lymphocyte mediated immunity
## 328 GO:0045454 1.767995e-05 8.228066 1.1635065 8 54 cell redox homeostasis
## 330 GO:0038096 5.938276e-06 8.120069 1.3290625 9 62 Fc-gamma receptor signaling pathway involved in phagocytosis
## 331 GO:0032956 6.844509e-09 8.054177 2.2930221 15 108 regulation of actin cytoskeleton organization
## 332 GO:0070527 8.429152e-04 7.761765 0.7541246 5 35 platelet aggregation
## 375 GO:0030183 2.977594e-04 7.533971 0.9309577 6 44 B cell differentiation
## 376 GO:0032943 1.042135e-04 7.410870 1.1056839 7 53 mononuclear cell proliferation
## 378 GO:0050766 1.363249e-03 6.882179 0.8360232 5 39 positive regulation of phagocytosis
## 379 GO:0034765 1.841498e-04 6.698528 1.2083801 7 57 regulation of ion transmembrane transport
## 393 GO:0002253 3.088878e-10 6.536693 3.9645614 21 191 activation of immune response
## 425 GO:0060337 1.734690e-03 6.480112 0.8812847 5 41 type I interferon signaling pathway
## 427 GO:0002479 9.718760e-05 6.297006 1.4651564 8 68 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent
## 433 GO:0031334 1.304847e-06 6.010205 2.5363073 13 119 positive regulation of protein complex assembly
## 438 GO:0019886 1.324089e-04 5.994867 1.5297956 8 71 antigen processing and presentation of exogenous peptide antigen via MHC class II
## 443 GO:0048584 2.512184e-10 5.766667 5.2222222 24 264 positive regulation of response to stimulus
## 446 GO:0051258 6.669386e-08 5.748960 3.5120660 17 163 protein polymerization
## 447 GO:0002250 7.003133e-05 5.737500 1.7932250 9 89 adaptive immune response
## 471 GO:0006909 7.778460e-05 5.654116 1.8175936 9 88 phagocytosis
## 472 GO:0002429 3.077802e-11 5.616730 5.9683575 27 277 immune response-activating cell surface receptor signaling pathway
## 476 GO:0098754 1.606547e-03 5.287931 1.2712386 6 59 detoxification
## 477 GO:0002504 6.840134e-04 5.276439 1.4915630 7 70 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
## 479 GO:0006959 1.724426e-03 5.204628 1.2880958 6 61 humoral immune response
## 480 GO:0006521 4.242904e-03 5.164706 1.0773209 5 50 regulation of cellular amino acid metabolic process
## 481 GO:0002460 4.270743e-03 5.149333 1.0781914 5 52 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
## 484 GO:1902600 1.873431e-03 5.115584 1.3092389 6 61 proton transmembrane transport
## 523 GO:0002474 1.043439e-03 4.879164 1.6000740 7 75 antigen processing and presentation of peptide antigen via MHC class I
## 525 GO:0002478 2.408688e-03 4.838849 1.3736332 6 67 antigen processing and presentation of exogenous peptide antigen
## 526 GO:0051130 5.062075e-04 4.827175 1.8555467 8 93 positive regulation of cellular component organization
## 532 GO:0060402 6.129486e-03 4.694643 1.1732429 5 55 calcium ion transport into cytosol
## 533 GO:0019882 1.281192e-03 4.691169 1.6555334 7 81 antigen processing and presentation
## 538 GO:0022900 7.490378e-05 4.608633 2.6933021 11 125 electron transport chain
## 573 GO:0031145 3.581638e-03 4.442942 1.4867028 6 69 anaphase-promoting complex-dependent catabolic process
## 576 GO:0060333 3.848907e-03 4.372966 1.5082492 6 70 interferon-gamma-mediated signaling pathway
## 579 GO:0098609 1.911971e-03 4.353422 1.7739883 7 85 cell-cell adhesion
## 580 GO:0034340 4.130695e-03 4.305143 1.5297956 6 71 response to type I interferon
## 587 GO:0002764 2.104463e-09 4.165994 8.7478454 30 406 immune response-regulating signaling pathway
## 618 GO:0016999 6.003360e-03 3.959759 1.6506098 6 77 antibiotic metabolic process
## 621 GO:0033209 6.518920e-03 3.887401 1.6790795 6 78 tumor necrosis factor-mediated signaling pathway
## 624 GO:0002684 7.959149e-09 3.832508 9.8491042 31 476 positive regulation of immune system process
## 629 GO:0043900 3.840052e-03 3.804842 2.0057811 7 95 regulation of multi-organism process
## 649 GO:0045055 7.933682e-08 3.658200 9.0943021 28 425 regulated exocytosis
## 650 GO:0002275 1.333342e-07 3.646473 8.7439340 27 408 myeloid cell activation involved in immune response
## 652 GO:0002444 3.738804e-07 3.634370 8.0602499 25 381 myeloid leukocyte mediated immunity
## 653 GO:0050852 8.781753e-04 3.630609 3.0270204 10 141 T cell receptor signaling pathway
## 654 GO:0051235 4.910157e-03 3.624709 2.0970391 7 98 maintenance of location
## 655 GO:0060071 1.624234e-02 3.622702 1.4867028 5 69 Wnt signaling pathway, planar cell polarity pathway
## 657 GO:0009308 1.690316e-02 3.583068 1.5016644 5 70 amine metabolic process
## 659 GO:0072593 2.954430e-03 3.580034 2.4337170 8 113 reactive oxygen species metabolic process
## 661 GO:0062012 9.638646e-03 3.555727 1.8228838 6 85 regulation of small molecule metabolic process
## 669 GO:0045321 7.288544e-06 3.521102 6.5522447 20 335 leukocyte activation
## 690 GO:0032946 1.041688e-02 3.491272 1.8529919 6 86 positive regulation of mononuclear cell proliferation
## 692 GO:0002700 1.099416e-02 3.447732 1.8745383 6 87 regulation of production of molecular mediator of immune response
## 693 GO:0043312 1.518767e-06 3.429410 8.1014528 24 376 neutrophil degranulation
## 694 GO:0070663 2.248484e-03 3.420472 2.8656735 9 133 regulation of leukocyte proliferation
## 696 GO:0002263 5.663606e-08 3.398117 11.2687762 32 523 cell activation involved in immune response
## 701 GO:0042119 2.307617e-06 3.339950 8.2953706 24 385 neutrophil activation
## 705 GO:0001736 2.251881e-02 3.309664 1.6159813 5 75 establishment of planar polarity
## 712 GO:0098660 4.315780e-05 3.272417 6.1838217 18 287 inorganic ion transmembrane transport
## 715 GO:0042773 2.369804e-02 3.262635 1.6375277 5 76 ATP synthesis coupled electron transport
## 732 GO:0002521 8.172597e-04 3.205571 4.1064629 12 194 leukocyte differentiation
## 733 GO:1903706 2.158449e-03 3.190212 3.4101342 10 159 regulation of hemopoiesis
## 738 GO:0032940 5.356758e-06 3.097913 9.3426058 25 443 secretion by cell
## 748 GO:0034764 3.018993e-02 3.046053 1.7452598 5 81 positive regulation of transmembrane transport
## 765 GO:0006874 2.987240e-03 3.038568 3.5641500 10 167 cellular calcium ion homeostasis
## 766 GO:0048871 1.173825e-02 3.034795 2.4702366 7 116 multicellular organismal homeostasis
## 767 GO:0060249 1.893626e-02 3.030153 2.1122360 6 100 anatomical structure homeostasis
## 775 GO:0071345 1.083652e-03 2.946677 4.8440581 13 254 cellular response to cytokine stimulus
## 779 GO:0002223 3.457392e-02 2.929263 1.8098990 5 84 stimulatory C-type lectin receptor signaling pathway
## 782 GO:0072507 1.745498e-03 2.911356 4.4816548 12 208 divalent inorganic cation homeostasis
## 784 GO:0038095 2.256059e-02 2.903476 2.1977345 6 102 Fc-epsilon receptor signaling pathway
## 785 GO:0030100 6.209547e-03 2.896889 3.3396947 9 155 regulation of endocytosis
## 793 GO:0010959 1.552403e-02 2.860136 2.6095450 7 122 regulation of metal ion transport
## 815 GO:0009607 3.273015e-04 2.837898 6.6337246 17 311 response to biotic stimulus
## 819 GO:0006873 5.405293e-04 2.796828 6.2915538 16 292 cellular ion homeostasis
## 820 GO:0097237 1.725583e-02 2.795640 2.6651467 7 125 cellular response to toxic substance
## 824 GO:0042180 1.196669e-02 2.772056 3.0811377 8 143 cellular ketone metabolic process
## 827 GO:0002831 4.271836e-02 2.753151 1.9176311 5 89 regulation of response to biotic stimulus
## 833 GO:0072511 4.523822e-03 2.694743 4.3954691 11 204 divalent inorganic cation transport
## 839 GO:1905330 4.627370e-02 2.688440 1.9607240 5 91 regulation of morphogenesis of an epithelium
## 859 GO:0098655 2.413617e-03 2.666381 5.2861744 13 251 cation transmembrane transport
## 861 GO:0045619 4.840683e-02 2.652192 1.9855609 5 93 regulation of lymphocyte differentiation
## 862 GO:0002244 3.244626e-02 2.651564 2.3916523 6 111 hematopoietic progenitor cell differentiation
## 888 GO:1903039 1.932803e-02 2.524357 3.3612411 8 156 positive regulation of leukocyte cell-cell adhesion
## 901 GO:0050878 3.321859e-02 2.416934 3.0531281 7 143 regulation of body fluid levels
## 918 GO:0007596 3.624460e-02 2.368567 3.1109741 7 145 blood coagulation
## 928 GO:0010638 2.387534e-03 2.329404 7.9297010 17 371 positive regulation of organelle organization
## 956 GO:0050867 1.873566e-02 2.266140 4.6755725 10 217 positive regulation of cell activation
## 972 GO:0032879 1.880473e-02 2.176833 5.3862389 11 264 regulation of localization
## 980 GO:0002758 3.206153e-02 2.155329 4.3954691 9 204 innate immune response-activating signal transduction
## 988 GO:0019725 8.987420e-03 2.115786 7.6031904 15 372 cellular homeostasis
## 996 GO:0070482 3.044516e-02 2.080000 5.0634080 10 235 response to oxygen levels
## 1013 GO:0001666 3.951471e-02 2.068253 4.5678404 9 212 response to hypoxia
##
## $B$up
## GOBPID Pvalue OddsRatio ExpCount Count Size Term
## 325 GO:0006614 6.394067e-09 8.943687 1.9465649 14 93 SRP-dependent cotranslational protein targeting to membrane
## 379 GO:0006413 4.571773e-08 7.505194 2.2601192 14 109 translational initiation
## 380 GO:0072599 4.587626e-08 7.502182 2.2605270 14 108 establishment of protein localization to endoplasmic reticulum
## 382 GO:0034097 1.060742e-03 7.300805 0.7904288 5 40 response to cytokine
## 391 GO:0000184 1.149301e-07 6.906737 2.4279734 14 116 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
## 427 GO:0048872 5.312813e-04 6.664103 1.0322339 6 51 homeostasis of number of cells
## 431 GO:0019222 3.450419e-07 6.079087 3.1744111 15 204 regulation of metabolic process
## 446 GO:0006612 6.712822e-07 5.880000 2.7954574 14 134 protein targeting to membrane
## 472 GO:0016070 4.609505e-05 5.480509 2.1371868 10 127 RNA metabolic process
## 520 GO:0019083 2.249698e-06 4.900293 3.5373061 15 169 viral transcription
## 523 GO:0002181 2.629101e-03 4.749673 1.3977287 6 67 cytoplasmic translation
## 593 GO:0006402 7.949142e-07 4.109288 5.6533465 20 272 mRNA catabolic process
## 600 GO:0017148 5.978342e-03 3.961341 1.6486787 6 79 negative regulation of translation
## 622 GO:0051048 4.115504e-03 3.751466 2.0302881 7 97 negative regulation of secretion
## 623 GO:0051092 2.341978e-03 3.726496 2.3442502 8 112 positive regulation of NF-kappaB transcription factor activity
## 624 GO:0048519 4.037364e-05 3.685226 5.1369740 16 302 negative regulation of biological process
## 625 GO:0001889 1.534560e-02 3.676923 1.4651564 5 70 liver development
## 626 GO:0007050 8.467947e-03 3.660572 1.7728119 6 85 cell cycle arrest
## 651 GO:1904950 5.140497e-03 3.590001 2.1140113 7 101 negative regulation of establishment of protein localization
## 652 GO:0048167 1.716174e-02 3.566260 1.5070180 5 72 regulation of synaptic plasticity
## 658 GO:0070498 1.014177e-02 3.511303 1.8419109 6 88 interleukin-1-mediated signaling pathway
## 664 GO:0007417 1.876509e-02 3.480645 1.5418219 5 75 central nervous system development
## 694 GO:0030522 2.193678e-02 3.331764 1.6045381 5 78 intracellular receptor signaling pathway
## 701 GO:0002262 1.413095e-02 3.248776 1.9789227 6 95 myeloid cell homeostasis
## 711 GO:1905475 9.818627e-03 3.148615 2.3861118 7 114 regulation of protein localization to membrane
## 736 GO:0051099 3.084855e-02 3.026011 1.7549759 5 84 positive regulation of binding
## 737 GO:0071216 7.936295e-03 2.994736 2.8675203 8 137 cellular response to biotic stimulus
## 738 GO:0051090 4.239697e-04 2.981419 5.5466634 15 265 regulation of DNA-binding transcription factor activity
## 740 GO:1903039 5.370654e-03 2.968057 3.2652056 9 156 positive regulation of leukocyte cell-cell adhesion
## 741 GO:0043484 2.074830e-02 2.962660 2.1558729 6 103 regulation of RNA splicing
## 773 GO:0032270 3.563571e-02 2.904003 1.8249319 5 95 positive regulation of cellular protein metabolic process
## 774 GO:0072657 5.601843e-04 2.899031 5.6993007 15 280 protein localization to membrane
## 776 GO:0033673 6.322052e-03 2.887952 3.3489288 9 160 negative regulation of kinase activity
## 780 GO:0043043 9.243884e-06 2.856679 10.8840187 27 520 peptide biosynthetic process
## 788 GO:0070304 4.171104e-02 2.771670 1.9047033 5 91 positive regulation of stress-activated protein kinase signaling cascade
## 809 GO:0045859 1.833423e-02 2.760109 2.6984127 7 136 regulation of protein kinase activity
## 810 GO:0034655 4.568297e-05 2.743696 9.9153903 24 475 nucleobase-containing compound catabolic process
## 819 GO:0002221 2.062224e-02 2.689031 2.7628663 7 132 pattern recognition receptor signaling pathway
## 821 GO:0090287 3.097210e-02 2.682357 2.3651810 6 113 regulation of cellular response to growth factor stimulus
## 823 GO:0070663 2.139719e-02 2.667348 2.7837971 7 133 regulation of leukocyte proliferation
## 851 GO:0043066 1.519838e-03 2.605183 6.2866146 15 306 negative regulation of apoptotic process
## 862 GO:0071559 4.259956e-02 2.471405 2.5535582 6 122 response to transforming growth factor beta
## 870 GO:0002791 3.026418e-02 2.468841 2.9929060 7 144 regulation of peptide secretion
## 875 GO:0051251 1.700681e-02 2.428750 3.9331363 9 189 positive regulation of lymphocyte activation
## 876 GO:0007283 1.705504e-02 2.427461 3.9349914 9 188 spermatogenesis
## 881 GO:0045785 2.478269e-02 2.401180 3.5222732 8 171 positive regulation of cell adhesion
## 882 GO:0009617 5.977864e-03 2.374085 5.8815563 13 281 response to bacterium
## 918 GO:0050867 1.559467e-02 2.338466 4.5419847 10 217 positive regulation of cell activation
## 922 GO:0060548 4.869073e-04 2.306653 11.5747353 24 553 negative regulation of cell death
## 924 GO:0000122 1.040857e-03 2.295477 10.0677173 21 481 negative regulation of transcription by RNA polymerase II
## 925 GO:0051338 5.836055e-04 2.274382 11.7212509 24 560 regulation of transferase activity
## 956 GO:0030098 2.983499e-02 2.186038 4.3391003 9 209 lymphocyte differentiation
## 960 GO:0045089 1.991976e-02 2.149117 5.4210786 11 259 positive regulation of innate immune response
## 979 GO:0043207 3.042520e-03 2.122553 10.2560946 20 490 response to external biotic stimulus
## 982 GO:0045937 3.442067e-03 2.097738 10.3691242 20 496 positive regulation of phosphate metabolic processgo_cell_type_filt_rbind <- map(go_cell_type_filt, function(l) {
bind_rows(l, .id = "directions")
})
names(go_cell_type_filt_rbind) <- c("Monocyte", "T-cell", "NK", "B-cell")
# openxlsx::write.xlsx(go_cell_type_filt_rbind, file = "results/tables/go_pbmc_by_cell_type.xlsx")
# Plot
excel_path <- "results/tables/go_pbmc_by_cell_type.xlsx"
sheets <- excel_sheets(excel_path)
go_df_l <- purrr::map(sheets, ~ read_excel(excel_path, sheet = .x, col_names = TRUE))
names(go_df_l) <- sheets
go_terms <- c("GO:0007159", "GO:0001916", "GO:0031343", "GO:0050853")
go_terms_df <- purrr::map2(go_df_l, go_terms, function(df, term) {
df[df$GOBPID == term, ]
})
go_df <- bind_rows(go_terms_df, .id = "cell_type")
go_terms_sorted <- c(
"positive regulation of T cell mediated cytotoxicity",
"positive regulation of cell killing",
"leukocyte cell-cell adhesion",
"B cell receptor signaling pathway"
)
go_df$Term <- factor(go_df$Term, levels = rev(go_terms_sorted))
go_df$cell_type <- factor(
go_df$cell_type,
levels = c("T-cell", "NK", "Monocyte", "B-cell")
)
palette2 <- c("#c20a35", "#aa2edc", "#71bdd0", "#bbaa2a")
go_gg <- ggplot(go_df, aes(Term, -1 * log10(Pvalue), color = cell_type)) +
geom_segment(aes(x = Term, xend = Term, y = 0, yend = -1 * log10(Pvalue))) +
geom_point() +
scale_color_manual(values = palette2) +
labs(x = "", y = "-log10 (p-value)", color = "") +
theme_light() +
coord_flip()
go_gg
# saveRDS(go_gg, "results/R_objects/ggplots/lollipop_go_enrichment_by_celltype_pbmc.rds")As we can see, there is a loss of function for each cell type.
6 Session Information
sessionInfo()## R version 3.6.1 (2019-07-05)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS High Sierra 10.13.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] forcats_0.5.0 stringr_1.4.0 dplyr_0.8.4 purrr_0.3.3 readr_1.3.1 tidyr_1.0.2 tibble_2.1.3 tidyverse_1.3.0 readxl_1.3.1 pheatmap_1.0.12 viridis_0.5.1 viridisLite_0.3.0 ggridges_0.5.2 ggrepel_0.8.1 topGO_2.38.1 SparseM_1.78 GO.db_3.10.0 GOstats_2.52.0 graph_1.64.0 Category_2.52.1 Matrix_1.2-18 GOplot_1.0.2 RColorBrewer_1.1-2 gridExtra_2.3 ggdendro_0.1-20 org.Hs.eg.db_3.10.0 AnnotationDbi_1.48.0 biomaRt_2.42.0 ggpubr_0.2.5 magrittr_1.5 Seurat_3.1.4 scran_1.14.6 scater_1.14.6 ggplot2_3.3.0 SingleCellExperiment_1.8.0 SummarizedExperiment_1.16.1 DelayedArray_0.12.2 BiocParallel_1.20.1 matrixStats_0.55.0 Biobase_2.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.0
## [43] IRanges_2.20.2 S4Vectors_0.24.3 BiocGenerics_0.32.0 BiocStyle_2.14.4
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.1 AnnotationForge_1.28.0 bit64_0.9-7 knitr_1.28 irlba_2.3.3 multcomp_1.4-12 data.table_1.12.8 RCurl_1.98-1.1 generics_0.0.2 metap_1.3 cowplot_1.0.0 TH.data_1.0-10 RSQLite_2.2.0 RANN_2.6.1 future_1.16.0 bit_1.1-15.2 mutoss_0.1-12 httpuv_1.5.2 xml2_1.2.2 lubridate_1.7.4 assertthat_0.2.1 xfun_0.12 hms_0.5.3 promises_1.1.0 evaluate_0.14 fansi_0.4.1 progress_1.2.2 caTools_1.18.0 dbplyr_1.4.2 Rgraphviz_2.30.0 igraph_1.2.4.2 DBI_1.1.0 htmlwidgets_1.5.1 RSpectra_0.16-0 crosstalk_1.0.0 backports_1.1.5 bookdown_0.18 annotate_1.64.0 gbRd_0.4-11 RcppParallel_4.4.4 vctrs_0.2.3 ROCR_1.0-7 withr_2.1.2 sctransform_0.2.1 prettyunits_1.1.1 mnormt_1.5-6 cluster_2.1.0
## [48] ape_5.3 lazyeval_0.2.2 crayon_1.3.4 genefilter_1.68.0 edgeR_3.28.1 pkgconfig_2.0.3 labeling_0.3 nlme_3.1-145 vipor_0.4.5 rlang_0.4.5 globals_0.12.5 lifecycle_0.1.0 sandwich_2.5-1 BiocFileCache_1.10.2 modelr_0.1.6 rsvd_1.0.3 cellranger_1.1.0 lmtest_0.9-37 zoo_1.8-7 reprex_0.3.0 beeswarm_0.2.3 png_0.1-7 bitops_1.0-6 KernSmooth_2.23-16 blob_1.2.1 DelayedMatrixStats_1.8.0 ggsignif_0.6.0 scales_1.1.0 memoise_1.1.0 GSEABase_1.48.0 plyr_1.8.6 ica_1.0-2 gplots_3.0.3 bibtex_0.4.2.2 gdata_2.18.0 zlibbioc_1.32.0 compiler_3.6.1 lsei_1.2-0 dqrng_0.2.1 plotrix_3.7-7 fitdistrplus_1.0-14 cli_2.0.2 XVector_0.26.0 listenv_0.8.0 patchwork_1.0.0 pbapply_1.4-2 MASS_7.3-51.5
## [95] mgcv_1.8-31 tidyselect_1.0.0 stringi_1.4.6 yaml_2.2.1 BiocSingular_1.2.2 askpass_1.1 locfit_1.5-9.1 grid_3.6.1 tools_3.6.1 future.apply_1.4.0 rstudioapi_0.11 farver_2.0.3 Rtsne_0.15 digest_0.6.25 BiocManager_1.30.10 shiny_1.4.0 Rcpp_1.0.3 broom_0.5.5 later_1.0.0 RcppAnnoy_0.0.15 httr_1.4.1 npsurv_0.4-0 Rdpack_0.11-1 colorspace_1.4-1 rvest_0.3.5 XML_3.99-0.3 fs_1.3.2 reticulate_1.14 splines_3.6.1 uwot_0.1.5 RBGL_1.62.1 statmod_1.4.34 sn_1.5-5 multtest_2.42.0 plotly_4.9.2 xtable_1.8-4 jsonlite_1.6.1 R6_2.4.1 TFisher_0.2.0 mime_0.9 pillar_1.4.3 htmltools_0.4.0 fastmap_1.0.1 DT_0.12 glue_1.3.1 BiocNeighbors_1.4.2 codetools_0.2-16
## [142] tsne_0.1-3 mvtnorm_1.1-0 lattice_0.20-40 numDeriv_2016.8-1.1 curl_4.3 ggbeeswarm_0.6.0 leiden_0.3.3 gtools_3.8.1 magick_2.3 openssl_1.4.1 survival_3.1-8 limma_3.42.2 rmarkdown_2.1 munsell_0.5.0 GenomeInfoDbData_1.2.2 haven_2.2.0 reshape2_1.4.3 gtable_0.3.0